CHAPTER 5. OVERVIEW OF THE EFFECTS ANALYSIS · Overview of the Effects Analysis Chapter 5 Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page i

Overview of the Effects Analysis Chapter 5

Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page i

CHAPTER 5. OVERVIEW OF THE EFFECTS ANALYSIS 1

Table of Contents 2

5.1 Introduction ...............................................................................................................................1 3 5.1.1 Regulatory Scope .....................................................................................................3 4 5.1.2 Spatial Scope ............................................................................................................4 5 5.1.3 Actions Evaluated ....................................................................................................4 6 5.1.4 Existing Biological Conditions ................................................................................4 7 5.1.5 Temporal Scope .......................................................................................................5 8 5.1.6 Approach to the Analysis .........................................................................................5 9

5.2 Status of the Effects Analysis ....................................................................................................7 10 5.3 Methodology ...........................................................................................................................11 11

5.3.1 Analytical Tools and Assumptions ........................................................................13 12 5.3.2 System-Level Analysis Approach to Support Assessments ..................................18 13 5.3.3 Fish Species Assessment Methods.........................................................................21 14 5.3.4 Killer Whale Analysis ............................................................................................25 15 5.3.5 Natural Community Assessment Methods .............................................................25 16 5.3.6 Covered Wildlife and Plant Species Assessment Methods ....................................28 17

5.4 Summary of Results ................................................................................................................29 18 5.4.1 Covered Fish Species .............................................................................................29 19 5.4.2 Natural Communities .............................................................................................73 20 5.4.3 Covered Wildlife and Plant Species ......................................................................84 21

22

23


Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page ii

List of Tables 1

Table 5-1. Summary of Impacts on the Extent of Natural Communities with Full BDCP 2 Implementation (i.e., conditions at the late long-term evaluation point) ..................116 3

Table 5-2. Summary of Conservation Provided for Natural Communities with Full BDCP 4 Implementation (i.e., conditions at the late long-term evaluation point) ..................117 5

Table 5-3. Summary of Impacts on the Extent of Covered Wildlife and Plant Species Habitats 6 with Full BDCP Implementation (i.e., conditions at the late long-term evaluation 7 point) .........................................................................................................................118 8

Table 5-4. Summary of Conservation Provided for Covered Wildlife and Plant Species with Full 9 BDCP Implementation (i.e., conditions at the late long-term evaluation point) ......124 10

List of Figures 11

Figure 5-1. Relationships Among Physical and Biological Modeling Results and 12 System-Wide ...............................................................................................................12 13

Figure 5-2. Process for Calculating Extent of BDCP Covered Activity and Conservation 14 Action Footprint Effects on Natural Communities and Covered Species Habitats ....27 15

Figure 5-3. Cumulative Riparian Habit Restoration versus Cumulative Permanent Removal ......77 16 Figure 5-4. Size Distribution of Affected Riparian Forest and Scrub Polygons ...........................78 17 Figure 5-5. Maturation and Succession of Restored Riparian Forest and Scrub and Use by 18

Covered Wildlife Species ...........................................................................................79 19 20


Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page 1

CHAPTER 5. OVERVIEW OF THE EFFECTS ANALYSIS 1

[Note to reviewers: The Effects Analysis is in progress and expected to be completed by the end 2 of January 2011. This chapter provides an overview of the Effects Analysis: its development and 3 context; a brief description of the methodologies used; the current status of the Effects Analysis; 4 and the summary of conclusions presented in the August 19, 2010 Working Draft and the 5 September 9, 2010 draft enhanced habitat analysis for covered fish species. These conclusions 6 are subject to modification as the revised analyses are being completed.] 7

5.1 INTRODUCTION 8

An effects analysis is the principal analytical component of a habitat conservation plan. It 9 presents conclusions regarding the expected outcomes of the conservation strategy and covered 10 activities. The analysis includes the effects of the proposed project on covered species, including 11 federally and state listed species, and other sensitive species potentially affected by the proposed 12 project. The effects analysis is a systematic, scientific look at the potential impacts of a proposed 13 project on these species and how these species would benefit from conservation actions. 14

This effects analysis provides a description of the outcomes of the BDCP Conservation Strategy 15 (Chapter 3) and covered activities (Chapter 4). The BDCP is being developed to promote the 16 recovery of endangered, threatened, and sensitive fish and wildlife species and their habitats in 17 the Sacramento-San Joaquin Delta in a way that will also protect and restore water supplies. 18

As described in Chapter 3, the Delta was once a vast marsh and floodplain intersected by 19 meandering channels and sloughs that provided habitat for a rich diversity of fish, wildlife, and 20 plants. The Delta of today is a system of artificially channeled and dredged waterways 21 constructed into static geometries, initially designed to support farming, and later, limited urban 22 development on Delta islands; to protect against flooding; and to convey water supplies to cities 23 and farms in the Bay Area, San Joaquin Valley and southern California. The physical 24 disturbances within the Delta, the introduction of nonnative species that have disrupted the 25 foodweb, along with multiple other environmental challenges to the ecosystem have contributed 26 to declines in fish, wildlife, and plant species and other organisms. In recent years, these factors 27 have caused a significant drop in the population of key native fish species, which has triggered 28 major reductions in water supply. 29

Developing the effects analysis is challenging because of the scale of changes to the Delta 30 ecosystem proposed in the BDCP Conservation Strategy. The approach embodied in the 31 conservation strategy reflects a significant departure from the manner in which at-risk Delta fish 32 and wildlife species and their habitats have been managed in the past. The BDCP approach 33 seeks to contribute to the restoration of the health of the ecological systems in the Delta by 34 focusing on ecological functions and processes on a broad landscape scale. Proposed actions 35 would result in fundamental, systemic, long-term physical changes to the Delta, such as 36 substantial alterations to water conveyance infrastructure and water management regimes and 37



extensive restoration of tidal, floodplain, and terrestrial habitats. Addressing such fundamental 1 and large-scale change has necessitated the use of a broad and complex analysis that has derived 2 new analytical tools and an expansion in ways of looking at the Delta system and its species. 3

The effects analysis is built on and reflects the extensive body of scientific investigation, study, 4 and analysis of the Delta compiled over several decades (see The State of Bay-Delta Science 5 2008), including the results and findings of numerous studies initiated under the CALFED Bay-6 Delta Science Program and Ecosystem Restoration Program, the long-term monitoring programs 7 conducted by the Interagency Ecological Program, research and monitoring conducted by state 8 and federal resource agencies, and research contributions of academic investigators. To ensure 9 that the BDCP would be based on the best scientific and commercial data available, the BDCP 10 Steering Committee also undertook a rigorous process to develop new and updated information 11 and to evaluate a wide variety of issues and approaches as it formulated a cohesive, 12 comprehensive Conservation Strategy. This effort included an evaluation in early 2009, 13 conducted by multiple teams of experts, of BDCP conservation options using the CALFED Bay-14 Delta Ecosystem Restoration Program’s Delta Regional Ecosystem Restoration Implementation 15 Plan (DRERIP) evaluation process. Implementation of the DRERIP evaluation process pulled 16 together a large group of scientific experts on various aspects of the Delta ecosystem and its 17 species and the information generated from the process provided some of the most advanced 18 thinking on the effects of conservation actions on key ecological stressors. Results of this 19 DRERIP evaluation were used, as applicable, to add support to various parts of the BDCP effects 20 analysis. 21

Over 60 species, 14 natural communities, and a broad range of ecological stressors are analyzed 22 in this effects analysis. Some of the species evaluated spend all or most of their lives in the 23 Delta; others spend only portions of their lives navigating their way through various parts of the 24 Delta via the water, land, or air. It is important to consider the effects of the BDCP on each 25 species over the whole of its life span, not just during individual life stages. 26

The aquatic effects analysis begins with an evaluation of how specific identified stressors could 27 potentially affect the various components of the ecosystem. The results of this analysis are used 28 in the analysis of individual fish species that is described in individual sections that follow and 29 address specific covered fish species. The terrestrial effects analysis begins with an analysis of 30 the effects of BDCP actions on natural communities in the Delta. Similar to the use of the 31 stressors analysis in the analyses of covered fish species, the results of the analysis of natural 32 communities is used in analyzing the effects on specific covered wildlife and plants that follow. 33 Each wildlife and plant species is assessed individually for the effects of BDCP actions and the 34 overall expected outcome for each species is summarized. 35

The analysis for each evaluation period is based on the physical and biological conditions 36 anticipated to be present with implementation of the BDCP actions at the end of each of the 37 timeframes described in the conservation measures in Chapter 3, Conservation Strategy, and the 38 implementation schedule in Chapter 6, Plan Implementation. The effects of climate change 39



(e.g., sea level rise, temperature, and hydrology) were evaluated for early and late points in time 1 of BDCP implementation based on climate change scenarios developed by the consultant team, 2 technical staff from the lead agencies, and outside climate change experts (see Appendix K, 3 Climate Change Evaluation Methods, for a discussion of this analysis). 4

The remainder of this section provides descriptions of the effects analysis regulatory scope, 5 spatial scope, actions evaluated, existing biological conditions, temporal scope, and approach to 6 the analysis. 7

5.1.1 Regulatory Scope 8

The effects analysis is designed to address the requirements of federal Endangered Species Act 9 (ESA) sections 10 and 7 and California Natural Community Conservation Planning Act 10 (NCCPA). Section 10 of the ESA requires that habitat conservation plans identify the impacts 11 likely to result from the proposed taking of federally listed threatened and endangered species. 12 Section 7 of the ESA requires a biological assessment be prepared that identifies the effects on 13 all federally listed threatened and endangered species likely to be affected by a federal action. 14 Section 7 of the ESA requires the effects analysis to evaluate all direct and indirect effects, 15 including the effects of interrelated and interdependent actions, on federal threatened and 16 endangered species and designated critical habitat1. The NCCPA requires that plans provide for 17 the conservation of covered species and natural communities. 18

The analysis addresses both federal and non-federal actions. Federal actions include all actions 19 by Reclamation, USFWS, and NMFS in the Plan Area and Central Valley Project (CVP) actions 20 upstream of the Delta that are interrelated and interdependent with BDCP actions. Chapter 4, 21 Covered Activities, includes descriptions of federal actions in the Plan Area. Federal actions 22 upstream of the Plan Area are described in the BDCP Biological Assessment [Note to Reviewers 23 – the BDCP Biological Assessment is expected to be prepared by Reclamation in 2011 and 24 would include a description of all CVP and Joint CVP/SWP actions that change as a result of 25 BDCP implementation]. Non-federal actions are all actions of the permit applicants under 26 Section 10 of the ESA permits and Section 2835 of the NCCPA permit in the Plan Area, 27 including changes in SWP operations upstream of the Delta that result from BDCP actions. 28

This effects analysis may also serve as part of the foundation for state and federal permitting and 29 approvals that will be needed from agencies such as the US Army Corps of Engineers (USACE), 30 US Environmental Protection Agency (EPA), and State Water Resources Control Board 31 (SWRCB) prior to implementing the conservation plan. 32

1 Effects of the action refers to the direct and indirect effects of an action on the species or critical habitat, together with the effects of other activities that

are interrelated or interdependent with that action, that will be added to the environmental baseline… Indirect effects are those that are caused by the proposed action and are later in time, but still are reasonably certain to occur. Interrelated actions are those that are part of a larger action and depend on the larger action for their justification. Interdependent actions are those that have no independent utility apart from the action under consideration. (50 CFR 402.02)



5.1.2 Spatial Scope 1

The analysis addresses the effects of BDCP implementation on covered species, designated 2 critical habitat, and essential fish habitat in the BDCP Plan Area2, upstream Delta tributaries, 3 CVP and State Water Project (SWP) reservoirs, and downstream of the Plan Area. The analysis 4 addresses the effects on NCCP natural communities for the Plan Area and upstream and 5 downstream of the Plan Area if natural communities could be affected by changes in water 6 operations. The Effects Analysis addresses all effects of BDCP implementation on all covered 7 species3 in the “action area” as defined under ESA regulations4. For information on Plan Area 8 boundaries and the distribution of biological resources within the Plan Area and in relevant 9 upstream and downstream locations see Chapter 2, Existing Ecological Conditions and Appendix 10 A, Covered Species Accounts. 11

5.1.3 Actions Evaluated 12

The analysis evaluates the construction of a new water diversion, isolated conveyance and other 13 water-related facilities, operations of current system components, dual operations of current and 14 proposed facilities, power plant operations, physical habitat restoration, protection and 15 enhancement of existing habitats, control of non-native species, and other actions described in 16 Chapter 3, Conservation Strategy, that address ecological stressors on the system and covered 17 species. Assumptions used in this analysis regarding the footprint locations of new conveyance 18 facilities and descriptions of construction-related activities (e.g., construction schedule, 19 construction methods) and maintenance activities and schedules for new facilities have been 20 provided by DWR. Full descriptions of conservation measures evaluated in the Effects Analysis 21 are in Chapter 3, Conservation Strategy. Full descriptions of covered activities evaluated in the 22 Effects Analysis are in Chapter 4, Covered Activities. 23

5.1.4 Existing Biological Conditions 24

The effects analysis evaluates how conservation measures and covered activities result in 25 changes to the existing biological conditions of the covered species and natural communities. 26 Existing biological conditions for natural communities are described in Chapter 2, Existing 27 Ecological Conditions and for covered species in Appendix A, Covered Species Accounts. The 28 Effects Analysis evaluates the aggregate effect on covered species of the environmental baseline5 29 and the implementation of the BDCP. 30

2 The BDCP Plan Area includes the legal Delta (as defined in California Water Code section 12220) Suisun Marsh, and the Yolo Bypass (see Chapter 1

Introduction for description and map location of Plan Area). 3 The southern resident killer whale is not a BDCP proposed covered species but is evaluated in the Effects Analysis because it is a listed species that is

potentially indirectly effected by BDCP actions 4 Action area means all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action. (50 CFR

402.02) 5 Under ESA regulations, the environmental baseline includes the past and present impacts of all Federal, State, or private actions and other human

activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation, and the impact of State or private actions which are contemporaneous with the consultation in process. (50 CFR 402.02)



5.1.5 Temporal Scope 1

Implementation of the BDCP is divided into two periods: 1) the “Near-Term” implementation 2 period is defined as the period before the North Delta Diversion Facilities become operable (i.e., 3 through-Delta conveyance operations only) and 2) the “Long-Term” implementation period is 4 defined as the period after the North Delta Diversion Facilities become operable (i.e., dual 5 conveyance operations). The effects analysis assesses the outcomes for covered species and 6 natural communities at three timeframes over the term of the BDCP: 7

1. Near-Term (NT) Evaluation Period: Effects from BDCP authorization through 8 approximately 10 years following approval (i.e., conditions during the period prior to 9 completion of construction of a new isolated conveyance facility and dual operations); 10

[Note to Reviewers: There are currently no proposed BDCP near-term water operational 11 criteria; therefore, the analysis is based on a continuation of the SWP and CVP 12 operations under existing authorizations. The effects of near term actions were evaluated 13 for all covered wildlife and plant species. For covered fish species, the NT period is not 14 called-out separately in the evaluation of operations (since operations are assumed not to 15 change from EBC), but NT effects on fish are evaluated for facilities construction (i.e., 16 intake structures). While overall habitat restoration effects on covered fish species are 17 included in this document, the more limited effects on fish of NT habitat restoration will 18 be provided in the enhanced habitat restoration evaluation currently underway.] 19

2. Early Long-Term (ELT) Evaluation Period: Effects from approximately 10 years 20 following BDCP authorization through approximately 15 years following authorization 21 (approximately 5 years after initiation of dual operations); and 22

3. Late Long-Term (LLT) Evaluation Period: Effects from approximately 15 years 23 following BDCP authorization through 50 years following authorization (the end of the 24 permit terms). 25

The analysis for each evaluation period is based on the physical and biological conditions 26 anticipated to be present with implementation of the BDCP actions at the end of each of the 27 timeframes as described in the conservation measures in Chapter 3, Conservation Strategy and 28 the implementation schedule in Chapter 6, Plan Implementation. The effects of climate change 29 (e.g., sea level rise, temperature and hydrology) on conditions within each timeframe were 30 evaluated for the early long-term and late long-term timeframes based on climate change 31 scenarios developed by the consultant team, technical staff from the lead agencies, and outside 32 climate change experts (see Appendix K, Climate Change Evaluation Methods). 33

5.1.6 Approach to the Analysis 34

The BDCP Effects Analysis utilized a broad range of analytical tools including hydrologic and 35 hydrodynamic models; temperature models; biological models for different life stages of covered 36 fish species; statistical relationships between physical conditions and covered fish species; 37



conceptual models for ecological conditions and individual fish species; and habitat models for 1 fish, wildlife, and plants. Some of these models were created and used for the first time in this 2 analysis. The methods used were developed in collaboration among technical experts from 3 USFWS, NMFS, DFG, Reclamation, and DWR and other experts on specific species addressed 4 and analytical tools used. 5

The specific location of and details of implementation approaches to most of the BDCP 6 conservation measures are not known and will not be known until BDCP is implemented through 7 an adaptive management process. As such, the level of adverse and beneficial effects on 8 biological resources were evaluated using reasonable assumptions regarding the potential 9 location and implementation approaches that could be applied during BDCP implementation. 10 Major types of assumptions used in the analysis are listed in Section 5.3.1.2. 11

The analysis was conducted using an ecologically scaled hierarchy. Changes to aquatic 12 ecosystem-level functions (e.g., flow, hydrodynamics, physical habitat restoration, food web 13 dynamics, toxic contaminants, and salinity) that are relevant to multiple fish species were 14 evaluated first. The results of these analyses were then used in the individual covered fish 15 species evaluations along with species-specific evaluation tools. In similar fashion, effects on 16 natural communities (e.g., estimating the extent of effects and effects on ecological processes, 17 gradients, and habitat function) were evaluated and the results were then used in the evaluation 18 of covered wildlife and plant species along with species-specific evaluation tools. 19

Covered fish species were evaluated using a broad range of available tools and best professional 20 judgment. Fish species were evaluated by specific life stages (e.g., egg/embryo, larvae, juvenile, 21 adult) and then the effects on all life stages were combined to synthesize a summary conclusion 22 of population and species level effects. In many cases, more than one tool or approach was used 23 to assess the effect of an ecological stressor on a fish species, providing a better understanding 24 the full range of potential outcomes and adding greater certainty to conclusions. Where there 25 was uncertainty regarding the use of an analytical tool or approach, the strengths and weaknesses 26 of the tool or approach were described. 27

Covered wildlife and plant species were evaluated mainly through the use of occurrence data and 28 geographic information system (GIS) based models of potentially suitable habitat developed 29 specifically for the BDCP. GIS was used extensively in spatially identifying the location of 30 existing species habitat and of proposed BDCP actions and in calculating the extent of overlap 31 between them. GIS proximity models were also developed and used to estimate disturbance 32 effects of covered activities on specific wildlife and plant species. 33

The analysis provides an estimate of effects on: 34

• covered species, where possible at the individual, population, and species levels, 35 including estimates of take; 36

[Note to Reviewers: Estimates of take have not been completed for covered fish species.] 37

• designated critical habitat; 38



• natural communities; 1

• Essential Fish Habitat (EFH)6. 2

Conclusions of the effects analysis are predictions based on current knowledge which has many 3 gaps and uncertainties. As a result, the level of scientific uncertainty is identified throughout the 4 methods, results, and conclusions discussions. 5

Climate change is an important factor in predicting the future biological conditions in the Delta 6 ecosystem and for covered species. The evaluation includes modeling of a range of possible 7 climate change outcomes for hydrology, sea level, and water temperature. Climate change 8 projections are included in the analysis as part of the aggregate effect of existing biological 9 conditions and the proposed BDCP on covered species. The analysis includes the evaluation of a 10 future with climate change but without implementation of BDCP to separate the effect of the 11 BDCP on ecological processes and species from the effects of climate change. 12

For each covered species, the summary conclusions consider the viability factors of abundance, 13 spatial distribution, population growth, and genetic diversity, along with the level of uncertainty, 14 in predicting the expected outcome. 15

5.2 STATUS OF THE EFFECTS ANALYSIS 16

The full effects analysis was initiated in early February 2010, after several years of discussions 17 and evaluations culminated in a set of conservation measures and long-term water operations 18 approved for purposes of analysis by the BDCP Steering Committee on January 29, 2010. 19 20 Discussions directly related to performance of the effects analysis were informally conducted 21 prior to June 2009 as consultants and federal (NMFS, USFWS, and Reclamation) and state 22 (DWR and DFG) agency staff began to formulate an approach to evaluate effects of the BDCP. 23 The basic approach to performing the effects analysis was developed between June and 24 November 2009. During this time, the consultants worked with federal and state agency staff to 25 discuss an approach to a combined effects analysis that would be used in preparation of the 26 following documents: 27

• BDCP HCP/NCCP; 28

• BDCP EIR/EIS biological resources section; 29

• BDCP biological assessment; and 30

• USFWS and NMFS biological opinions. 31

6 Under the Magnuson-Stevens Act, essential fish habitat for federally managed fish species is defined as "those waters and substrate necessary to fish for

spawning, breeding, feeding, or growth to maturity." Chinook salmon are the only BDCP covered species identified for management under this Act.



A “mini-effects analysis” for the covered fish species was conducted between November 2009 1 and January 2010 with the charge of identifying major issues in the proposed conservation 2 strategy being considered at that time and elevating these issues to the BDCP Steering 3 Committee. The mini-effects analysis evaluated the effects of proposed water operations and a 4 set of proposed habitat restoration and other stressors conservation measures identified at 5 Steering Committee meetings during summer and fall 2009. The analysis process was directly 6 overseen by the Effects Analysis Managers, a group of policy-level individuals initially from the 7 five federal and state agencies and PREs, and later joined by NGOs. The mini-effects analysis 8 evaluated the effects of the BDCP only on covered fish species and was divided into three 9 interactive groups: foodweb and water quality, anadromous fish, and pelagic fish. These groups 10 were composed of technical experts that were selected by Effects Analysis Managers from 11 agencies, NGOs, PREs, and consultants. The analysis process consisted primarily of weekly 12 meetings of each group to discuss and document the effects of proposed actions on the covered 13 fish species. Between meetings, group members conducted analyses and wrote results, and 14 presented their findings at the next meeting. The results were documented as a set of tables for 15 each species that were organized by lifestage and stressor. 16

The results of the mini-effects analysis were discussed at Steering Committee meetings in 17 January 2010. While the mini-effects analysis concluded that the project was mostly beneficial, 18 several areas of scientific disagreement were identified. As a result, the Steering Committee 19 made minor revisions to the proposed conservation strategy. 20

Early in February 2010, the full effects analysis was initiated to evaluate the revised 21 Conservation Strategy, with the exception of the near-term operational criteria, which were still 22 under development. The full effects analysis includes the evaluation of the BDCP on covered 23 fish, plant, and wildlife species as well as covered natural communities. Methodologies for the 24 analyses were discussed with technical experts from federal and state agencies, NGOs, and PREs 25 through June 2010. Preliminary results of these analyses were presented to Effects Analysis 26 Managers between May and July. Preliminary results of the effects analysis for covered wildlife 27 and plant species and natural communities were also presented at the July 15, 2010 Steering 28 Committee meeting. The Working Draft Effects Analysis was delivered to the Effects Analysis 29 Managers on August 19, 2010. 30

The five agencies (NMFS, USFWS, Reclamation, DFG, and DWR) reviewed the 31 August 19, 2010 Effects Analysis. The consultants reviewed and are addressing comments that 32 were provided to them in writing; and entered into extensive discussions with the agencies, 33 PREs, and NGOs regarding areas of significant scientific disagreement. In an effort to reach 34 resolution regarding areas of scientific disagreement, a series of “theme team” meetings occurred 35 during September and October 2010. 36

Two “theme teams” were established, one for anadromous fish and one for pelagic fish species. 37 These “theme team” meetings included technical staff from each of the agencies and the 38 consultant team, and were joined by representatives from the PREs and NGOs. These teams 39



were overseen by an Oversight Committee whose composition included the BDCP Management 1 Team and managers from the each of the five agencies, PREs and NGOs. Each meeting was led 2 by three managers, one from the federal agencies, one from the state agencies, and one from the 3 consultant team. The three managers reported regularly to the Oversight Committee regarding 4 the status of the scientific discussions at the theme team meetings. 5

The charge to the “theme teams” was to air and resolve major issues with the effects analysis. 6 Issues that could not be resolved within the “theme team” process, either because of significant 7 technical disagreement or because the issues required policy-level decisions, were to be elevated 8 to the Oversight Committee for additional discussion and resolution by high level agency 9 managers. In late October, a new process evolved as the Oversight Committee began to discuss 10 possible refinements to the BDCP Conservation Strategy based on the review of the aquatic 11 effects analysis and subsequent “theme team” discussions and efforts. 12

To date, the following six items have been identified as requiring further consideration and 13 evaluation by the Effect Analysis Oversight Committee. The first item, North Delta intake 14 configuration, was partially resolved at the November 10, 2010 Oversight Committee meeting, 15 where it was agreed that an on-bank configuration of north Delta intakes would be analyzed for 16 the January 31, 2011 Draft Effects Analysis. 17

1. North Delta intake configuration 18 Near-shore, in-river intakes in the north Delta create increased predator habitat. This is 19 predicted to have large predation effects on juvenile salmonids. An onshore intake 20 design will greatly reduce the adverse effects of predation of the design evaluated in the 21 effects analysis. A decision was made at the November 10, 2010 Oversight Committee 22 meeting to analyze an on-bank configuration for the January 31, 2011 Draft Effects 23 Analysis. Refinements to the locations and sizes of intakes are also under consideration. 24

2. Increased spring-run salmon egg mortality 25 Approximately 10 percent of the spring-run Chinook salmon population spawns in the 26 Sacramento River. Preliminary modeling results indicate that water temperatures could 27 potentially cause a 10 percent increase in spring-run Chinook salmon egg mortality 28 during wet, below normal, and above normal water year types for the 10 percent of the 29 population that spawns in the Sacramento River. Increased cold water pool storage, 30 Sacramento River flows, or habitat expansion in the tributary main spawning areas could 31 be used to address these effects. 32

3. Reduced Sacramento River flows downstream of the intakes 33 Flows are reduced downstream of the north Delta diversion facilities during spring, 34 summer, and fall in wet, above normal, and below normal water years. This may have an 35 effect on migratory cues of adult anadromous fish species, and possibly increase straying 36 into other adjacent watersheds. The biological importance of reduced flows and whether 37 migratory cues would in fact be affected is uncertain. There is also some debate 38



regarding the extent that reduced flows are a result of modeling assumptions rather than 1 changes in the future environment. 2 3

4. April-May south Delta operations potentially effecting Delta smelt 4 OMR flows in April and May would be modified by the proposed BDCP long-term 5 operations, as compared to the operations described in the existing biological opinions. 6 There is significant scientific disagreement regarding the relationship between OMR 7 flows and entrainment in the CVP and SWP facilities. There is also debate about the 8 biological importance of the predicted entrainment, specifically in regard to whether the 9 predicted entrainment of the juvenile life stage would have a population level effect. The 10 effect of any change is particularly uncertain since the OMR flows are less negative 11 during the adult life stage. 12

5. Spring X2/outflow effects on longfin smelt 13 The X2 location is higher (more easterly) in winter and spring months, which may 14 negatively affect longfin smelt abundance according to a statistical correlation between 15 X2 and longfin smelt abundance. The biological mechanism responsible for this 16 relationship is unknown and the relationship itself has degraded in the past 20 years, 17 likely due to a reduction in the available food supply. It is further anticipated that the 18 proposed project would enhance the productivity of the Delta through the restoration of 19 tidal habitat, thereby benefiting the species. The scientific uncertainty surrounding these 20 issues requires further evaluation. 21

6. Fall X2 - Changes in hydrodynamics potentially affecting delta smelt 22 The Fall X2 Reasonable and Prudent Alternative (RPA) action in the existing Biological 23 Opinions has never been adopted by Reclamation and it has never been implemented. 24 Nevertheless, if one assumes that Fall X2 is in the baseline and compares that to the 25 proposed project without the objective, the X2 position is higher (more easterly) in fall 26 and summer months in the above normal and wet water years. There is an ongoing 27 debate over whether this effect is biologically relevant to delta smelt. If the location of 28 Fall X2 is a meaningful indicator of habitat, then moving X2 upstream would reduce the 29 volume of available Delta smelt habitat. However, there is substantial scientific evidence 30 suggesting that X2 is not a meaningful indicator of habitat and that the analysis upon 31 which the RPA was based is technically flawed. It is further anticipated that habitat 32 restoration will contribute to increasing habitat for delta smelt while also increasing the 33 available food supply in key areas of the Delta. As there is scientific uncertainty 34 surrounding these issues, further evaluation is required. 35

The aforementioned issues will be the subject of further analysis after the release of the 36 November 2010 document. Moreover, to ensure that the final effects analysis is sufficiently 37 rigorous, comprehensive and complete, the technical discussions between the state and federal 38 agencies, PREs and NGOs will continue throughout the development of the effects analysis and 39



related documentation. Potential refinements are anticipated to be incorporated into the final 1 BDCP effects analysis for the proposed project, which is expected in early 2011. 2

5.3 METHODOLOGY 3

This section provides a summary of methods used to conduct the August 19, 2010 Draft Effects 4 Analysis and the September 9, 2010 Draft Enhanced Habitat Analysis for covered fish species. 5 It contains short descriptions of analytical tools, assumptions, and specific analytical approaches. 6 These methods were developed largely in collaboration with technical experts from USFWS, 7 NMFS, DFG, Reclamation, DWR and others. The effects analysis is divided into aquatic and 8 terrestrial analyses with little overlap. Aquatic methods consist of initial physical modeling 9 based on operating criteria agreed to at the January 29, 2010 Steering Committee meeting that 10 fed inputs into biological models and system wide analyses, such as water quality, toxics, and the 11 aquatic foodweb (Figure 1). Biological models and system-wide analyses informed species and 12 lifestage evaluations. For terrestrial species, the effects of the BDCP on natural communities 13 were evaluated primarily using GIS analysis with some physical model outputs (Figure 5-1). 14 GIS, species habitat models, and output from natural community-level analyses were used to 15 evaluate effects on individuals covered wildlife and plant species. 16



1 *The Fall X2 model was included in the August 19 draft analysis because it was identified by USFWS as an RPA action in the current delta smelt biological opinion. However, 2

the biological importance of any changes in the position of X2 in the fall is the topic of significant scientific dispute, and is the subject of further analysis. 3 Figure 5-1. Relationships Among Physical and Biological Modeling Tools and System-Wide and Species-Level Evaluations for the BDCP Effects Analysis



The BDCP was divided into three evaluation periods for the Effects Analysis, near-term, early 1 long-term and late long-term (Section 5.1). The August 19, 2010 Draft Effects Analysis only 2 included evaluations during the early late long-term periods because near-term water operations 3 had not yet been agreed upon. 4

The proposed project was modeled with predicted future climate change for the early long-term 5 and late long-term periods. As a result, the existing biological conditions to which the proposed 6 project was compared also included climate change predictions for the early long-term and late 7 long-term evaluation periods. To determine the effects of the BDCP on a specific parameter 8 without incorporating the effects of future climate change, the results of that parameter for the 9 existing biological conditions scenario was compared to that of the proposed project during the 10 same evaluation period. 11

5.3.1 Analytical Tools and Assumptions 12

5.3.1.1 Analytical Tools 13

Several types of analytical tools were used in performance of the aquatic effects analysis. These 14 analytical tools can be categorized as physical and biological. Figure 5-1 summarized the 15 relationships between the various analytical tools and biological evaluations used in the effects 16 analysis. The following sections briefly describe the models, their outputs and use in the effects 17 analysis. 18

5.3.1.1.1 CALSIM II 19

The CALSIM II planning model simulates the operation of the CVP and SWP over a range of 20 hydrologic conditions. CALSIM II produces key outputs that include river flows and diversions, 21 reservoir storage, Delta flows and exports, Delta inflow and outflow, deliveries to project and 22 non-project users, and controls on project operations. Inputs to CALSIM II include water 23 diversion requirements (demands), stream accretions and depletions, rim basin inflows, irrigation 24 efficiency, return flows, non-recoverable losses, groundwater operation, and in-Delta operating 25 criteria. In-Delta operating criteria for intake bypass flows, Sacramento River pulse flows, Delta 26 Cross Channel operations, X2 standards, water quality standards, Yolo Bypass spills, and south 27 Delta exports and flows that were agreed to at the January 29, 2010 Steering Committee were 28 used as model inputs. Sacramento Valley and tributary rim basin hydrologies were developed 29 for CALSIM II using a process designed to adjust the historical sequence of monthly stream 30 flows over an 82-year period (1922 to 2003) to represent a sequence of flows at a future level of 31 development. As can be seen in Figure 5-1, CALSIM II outputs were used as the basis for other 32 physical and biological models and analyses. 33

5.3.1.1.2 DSM 2 34

DSM2 is a one-dimensional hydrodynamic and water quality simulation model used to simulate 35 hydrodynamics, water quality, and particle tracking in the Sacramento-San Joaquin 36



Delta (DWR 2002). The DSM2 model has three separate components, or modules: HYDRO, 1 QUAL, and PTM. 2

DSM-HYDRO simulates velocities and water surface elevations and provides the flow input for 3 QUAL and PTM. DSM2-HYDRO predicts changes in flow rates and depths as a result of the 4 BDCP and climate change. Outputs were used to determine the effects of these hydrodynamic 5 parameters on covered terrestrial and fish species and as inputs to other biological models. 6

The DSM-QUAL module simulates fate and transport of conservative and non-conservative 7 water quality constituents, including salts, given a flow field simulated by HYDRO. Outputs 8 were used to estimate changes in salinity and their effects on covered species as a result of the 9 BDCP and climate change. Outputs of this model were used in the system-wide analysis of 10 toxics. 11

An add-on to the DSM-QUAL module, the nutrient model, predicts the effects of changes to 12 hydrology on temperature, dissolved oxygen, nitrogen and phosphorus concentrations (including 13 speciation of each), and algal production. Outputs were used in the system-wide analyses for 14 water quality, the aquatic foodweb, and toxics. 15

The DSM-PTM module simulates fate and transport of neutrally buoyant particles through space 16 and time. Outputs were used to estimate the effect of hydrodynamic changes on the fate and 17 transport of larval fish and toxics through the Delta. 18

5.3.1.1.3 RMA Model 19

The RMA model is a generalized free surface hydrodynamic model that is used to compute two-20 dimensional depth-averaged velocity and water surface elevation. The model uses CALSIM 21 outputs as well as existing bathymetry and topography as inputs. The RMA model output was 22 used to evaluate the effects tidal habitat restoration on flows throughout the Delta and the 23 subsequent effects on covered species. 24

5.3.1.1.4 Upper Sacramento River Water Quality Model (USRWQM) 25

The USRWQM uses the HEC-5Q model to simulate mean daily (using 6-hour meteorology) 26 reservoir and river temperatures at key locations on the Sacramento River. After being 27 temporally downsized to daily average flows, monthly flows from CALSIM II for an 82 year 28 period (WY 1922-2003) are used as input into the USRWQM. Output from the USRWQM was 29 used as an input to a number of biological models for upstream lifestages of salmonids and 30 sturgeon. 31

5.3.1.1.5 Reclamation Temperature Model 32

The Reclamation Temperature Model is a reservoir and stream temperature model that simulates 33 monthly reservoir and stream temperatures for evaluating the effects of CVP/SWP project 34 operations on mean monthly water temperatures in the Feather, Stanislaus, Trinity, Sacramento, 35



and American river basins and upstream reservoirs based on hydrologic and climatic input data. 1 The model uses CALSIM II output. The Reclamation Temperature Model was used to predict 2 the effects of operations on water temperatures in the Feather, Stanislaus, Trinity, and American 3 river basins, which were then used as inputs to the Reclamation Salmon Mortality Model and 4 species-specific habitat evaluations. 5

5.3.1.1.6 MIKE-21 6

The MIKE-21 flexible mesh model is a two-dimensional hydrodynamic model that predicts 7 changes in water surface elevation, flow, and average velocity in the Yolo Bypass as a result of 8 inundation under CM14 Yolo Bypass Fisheries Enhancements. The model incorporates existing 9 LiDAR and Toe Drain/Tule Canal bathymetry as well as estimated west-side tributary flows. 10 Outputs were used to predict the potential benefits to species that use the Yolo Bypass as habitat 11 when inundated (e.g., splittail, Chinook salmon) and to food production. 12

5.3.1.1.7 Delta Regional Ecosystem Restoration Implementation Plan (DRERIP) 13

The DRERIP conceptual models and scientific evaluation process were developed to aid in 14 planning and decision making for potential ecosystem restoration actions in the Delta. 15 Conceptual models contain background biological information on covered species and their 16 stressors. The DRERIP scientific process was used twice for BDCP, once for a coarse-level 17 evaluation of draft conservation measures in late 2008, then for a full evaluation of draft 18 conservation measures in early 2009. Results of these previous evaluations, as well as the 19 conceptual models themselves, were used for qualitative assessments and best professional 20 judgment throughout the effects analysis. 21

5.3.1.1.8 Striped Bass Bioenergetic Model 22

A striped bass bioenergetic model was developed to estimate predation by striped bass based on 23 water temperature, striped bass size, and the density and size of prey encountered. Inputs to the 24 model include water temperature, prey density, and striped bass fork lengths taken from 25 historical data for the Delta. This model was used to estimate predation rates of striped bass on 26 covered fish species at the proposed North Delta diversion intakes. Results of the model were 27 also used as inputs to the Delta Passage Model and Interactive Object-Oriented Salmon 28 Simulation (IOS) Model. 29

5.3.1.1.9 Delta Passage Model 30

The Delta Passage Model (DPM) simulates migration and mortality of juvenile Chinook salmon 31 entering the Delta from the Sacramento, Mokelumne, and San Joaquin rivers through a 32 simplified Delta channel network similar to that depicted in Perry et al. (2010), and provides 33 quantitative estimates of relative juvenile Chinook salmon survival through the Delta to Chipps 34 Island. The DPM is based on a detailed accounting of migratory pathways and reach-specific 35 mortality as smolts travel through a network of Delta channels. The model uses input from 36 CALSIM II, DSM2-HYDRO, and the bioenergetics model to estimate predation pressure on 37



juvenile salmon. The model was used to predict relative reach-specific survival estimates for 1 winter, spring, and fall-run juvenile Chinook salmon passing through the Delta. 2

5.3.1.1.10 Interactive Object-Oriented Salmon Simulation (IOS) Model 3

The IOS model is a spatially explicit winter-run Chinook salmon life cycle model that examines 4 environmental effects of multiple parameters on the abundance, size, and survival of winter-run 5 Chinook salmon through successive life-stages. The IOS model uses simulated upstream daily 6 flow and water temperatures from USRWQM and in-Delta flows from DSM2 as inputs. The 7 model was used to evaluate the effects of multiple aspects of the BDCP on survival of winter-run 8 Chinook salmon and population viability. 9

5.3.1.1.11 Oncorhynchus Bayesian Analysis (OBAN) Model 10

The OBAN model is a winter-run Chinook salmon life cycle analytical framework used to 11 predict the effects of multiple actions on winter-run Chinook salmon by incorporating various 12 sources of mortality in all phases of the life history. The model uses simulated upstream daily 13 flow and water temperatures from USRWQM. Complementary to IOS, OBAN was used to 14 predict the effects of multiple BDCP actions on winter-run Chinook salmon survival and 15 population dynamics and population viability. 16

5.3.1.1.12 Sacramento River Ecological Flows Tool (SacEFT) 17

The SacEFT model is a database-centered software system for linking flow management actions 18 to changes in the physical habitats for several focal species of concern. The model employs a set 19 of functional relationships to generate habitat-centered performance measures for all races of 20 Chinook salmon, steelhead, and green sturgeon that change in response to flow management 21 scenarios. The model uses daily temperature and flow outputs from the USRWQM. SacEFT 22 was used to predict the effects of flow changes in the Sacramento River on a set of physical 23 (spawning area, juvenile rearing area, redd scour, and redd dewatering) and biological (egg 24 survival, juvenile stranding, and juvenile growth) parameters for all races of Chinook salmon and 25 steelhead. The model also predicted flow-based effects on green sturgeon egg survival. 26

5.3.1.1.13 SALMOD 27

SALMOD estimates both anadromous and resident juvenile salmonid production in freshwater, 28 as a result of habitat. Habitat area (quantified as weighted usable area or WUA) is computed 29 from flow versus microhabitat area functions developed empirically or by using Physical Habitat 30 Simulation (PHABSIM) software or a similar physical habitat model. The inputs to the model 31 include CALSIM flows, water temperature from USRWQM, spawning distribution based on 32 aerial surveys, spawning timing depending on salmon race, and the number of spawners 33 provided by the user (e.g., recent average escapement). SALMOD was used to predict the 34 effects of flows in the Sacramento River on habitat quality and quantity and ultimately on 35 juvenile production of all races of Chinook salmon. 36



5.3.1.1.14 Reclamation Salmon Mortality Model 1

This model uses temperature exposure mortality criteria resulting from changes in water 2 operations for the three life stages, spawning distribution data, and output from the river 3 temperature models to estimate percentages of egg and fry losses of a given brood of eggs for 4 each run of Chinook salmon. The model uses water temperature output from the USRWQM for 5 the Sacramento River; and the Reclamation Temperature Model for other Trinity, Feather, 6 American, and Stanislaus rivers. The model was used to predict temperature-related proportional 7 losses of eggs and fry for each race of Chinook salmon in the Trinity, Sacramento, Feather, 8 American, and Stanislaus rivers. 9

5.3.1.1.15 Fall X2 Model 10

Delta smelt abiotic habitat during fall (September-December) has been calculated as surface area 11 and related to the position of X2 (Feyrer et al. 2007). The use X2 position as an indicator of 12 delta smelt habitat, and the technical basis for this analysis (Feyrer, et. Al. 2007), are the subject 13 of significant scientific debate. The model was used nevertheless in the effects analysis because 14 it was an RPA action identified by the USFWS in the current biological opinion. The statistical 15 relationship was also modified based on BDCP proposed habitat restoration. 16

Covered Wildlife and Plant Species Habitat Models 17

As part of the BDCP analysis, habitat models were developed for each of the covered wildlife 18 and plant species based on vegetation/land cover associations that support each species’ habitat 19 type and the spatial requirements (e.g., minimum habitat patch size that can support use by a 20 species, proximity to other habitat areas that is necessary to support species use) of each species. 21 Descriptions of the components of each species habitat model (i.e., the GIS vegetation/land cover 22 types and other assumptions used to define each covered species habitat types) and maps of each 23 species modeled are presented in Appendix A, Covered Species Accounts. 24

5.3.1.2 Major Assumptions 25

The BDCP effects analysis relies on many assumptions regarding how the physical and 26 biological processes of the Plan Area function and support natural communities and covered 27 species; how restored habitats will develop over time; and how the physical and biological 28 processes, natural communities, and covered species will respond to implementation of the 29 conservation measures over time. These assumptions represent a reasonable interpretation of the 30 best available information regarding how the Delta ecosystem functions and the life history 31 requirement of the covered species. These assumptions are continuing to be refined and 32 improved as new information is generated through the BDCP planning process. 33

34



Major assumptions used to conduct the effects analysis have been formulated for the following 1 topic areas: 2

• The schedule for implementing conservation measures (from the implementation 3 schedule presented in draft Chapter 6, Implementation Plan); 4

• Footprint locations and extents for habitat restoration/enhancement and other stressors 5 conservation measures used to calculate effects on existing natural communities and 6 habitat, effects on water quality and hydrodynamic conditions, and to model the extent of 7 future restored tidal habitat; 8

• Habitat restoration and enhancement designs and the development of restored and 9 enhanced habitat functions; 10

• Future effects of sea level rise; 11

• Types of and locations for implementing nonnative predator control actions and the 12 effectiveness of such actions; 13

• Effectiveness of non-physical fish barrier and methylmercury control actions; 14

• Extent, frequency, and effectiveness of nonnative aquatic vegetation control actions; 15

• Location and effects of conveyance facilities construction and maintenance activities; 16

• Types and effectiveness of Yolo Bypass fisheries enhancement actions; 17

• Effects of restoration and construction-related noise and visual disturbances on covered 18 wildlife species. 19

5.3.2 System-Level Analysis Approach to Support Assessments 20

5.3.2.1 Physical Modeling 21

To support the effects analysis, physical modeling is required to evaluate changes to conditions 22 affecting resources within the Delta as well as effects to upstream and downstream resources. 23 Hydrologic, operations, hydrodynamics, water quality, and particle tracking analyses are 24 required to provide baseline and comparative information for habitat, fisheries, water supply, and 25 water quality assessments. These analyses are also required to assess changes in the function of 26 the Proposed Project under varying assumptions of future, non-project conditions such as climate 27 change, future demands, and changes in Delta landforms (planned and unplanned). 28

The BDCP physical modeling can be separated into the following major elements: 29

1. Climate and Sea Level Change Scenarios; 30

2. Regional Hydrologic Modeling; 31

3. Hydrology and Systems Operations Modeling; 32



4. Yolo Bypass Floodplain Hydraulics; 1

5. Reservoir and River Temperature Modeling; 2

6. Delta Hydrodynamics and Water Quality Modeling; and 3

7. Delta Particle Transport and Fate Modeling. 4

Climate and sea level change analysis was conducted using a set of climate change scenarios that 5 were spatially downscaled and entered into the regional Variable Infiltration Capacity (VIC) 6 hydrologic model. This macro-scale model translated the effects of future climate conditions on 7 watershed processes ultimately affecting the timing and volume of runoff. Results from this 8 model informed hydrologic and system operations modeling, which was conducted using 9 CALSIM II. As shown in Figure 5-1, CALSIM II formed the base of hydrologic modeling from 10 which multiple hydrologic, hydrodynamic, and biological models and analyses received inputs. 11 Yolo Bypass floodplain hydraulics were predicted using MIKE-21, a two-dimensional modeling 12 for the Yolo Bypass, and CALSIM II output to better understand inundation characteristics under 13 modifications to the Fremont Weir. For upstream out-of-Delta analyses, CALSIM II outputs 14 were entered into the USRWQM, which calculated daily flows and water temperatures in the 15 upper Sacramento River and the Reclamation Temperature Model, which calculates monthly 16 averaged reservoir and river temperatures in multiple upstream rivers and reservoirs. Outputs of 17 USRWQM were used in a number of biological models and analyses to determine the effect of 18 flows and water temperature on anadromous fish species migration and survival. In the Delta, 19 CALSIM II outputs informed Delta hydrodynamics and water quality modeling such as the 20 RMA model, DSM2-HYDRO and DSM2-QUAL. These models were used to predict the effects 21 of the BDCP on to tidal stage, velocity, flows, and salinity in the Delta. CALSIM II outputs also 22 informed Delta particle transport and fate modeling using DSM2-PTM. 23

5.3.2.2 Food Web 24

The BDCP is predicted to affect the Bay-Delta foodweb in two primary ways: (1) changes to 25 hydrology and hydrodynamics in Delta channels; and (2) restoration of tidal marsh, riparian, 26 channel margin, and floodplain. To evaluate the effect of hydrology and hydrodynamics, the 27 DSM2-QUAL nutrient model was used to estimate algal production. The effects of habitat 28 restoration on the foodweb was estimated using existing data from within and outside the Delta, 29 and best professional judgment was used to estimate the effects on covered fish species. 30

5.3.2.3 Toxics 31

There were six toxicants deemed important to the Delta aquatic community and, therefore, 32 analyzed for the effects analysis: mercury, selenium, pyrethroids, endocrine disrupting 33 compounds, copper, and ammonia/um. 34

The BDCP is predicted to affect mercury loads and methylmercury production as a result of 35 three actions: (1) water operations, (2) tidal habitat restoration, and (3) enhanced Yolo Bypass 36



inundation. The effects of the BDCP water operations on mercury were evaluated using 1 DSM-QUAL source water fingerprinting outputs. The proportion of water predicted from 2 DSM-QUAL from the Sacramento River and San Joaquin River at two locations in the Delta was 3 multiplied by historical mercury loads calculated for water from each river. To determine the 4 effects of tidal habitat restoration on methylmercury loads, average rates of methylation in 5 wetlands and open water areas from the Delta mercury TMDL were multiplied by the area (in 6 acres) of restored habitat and floodplain to determine estimates of overall production of 7 methylmercury in project areas. To determine the effects of Yolo Bypass inundation on 8 methylmercury loads, the empirical relationship between net methylmercury production in Yolo 9 Bypass and outflow from Foe et al. (2008) was applied to the frequency duration using 10 CALSIM II output and area of inundated land using MIKE-21 output to determine the overall 11 change in net methylmercury production as a result of increased inundation of the Yolo Bypass. 12

The BDCP is predicted to affect selenium loads by changing the hydrology of the Delta such that 13 the proportion of water entering the Delta from the San Joaquin versus the Sacramento River will 14 be altered. This effect was analyzed using the source water fingerprinting method described for 15 methylmercury. 16

The BDCP is expected to result in regional changes in pyrethroid concentrations as a result of 17 changes in hydrodynamics. While the BDCP is not a source of increased pyrethroid loading, it 18 may affect dilution flows both positively and negatively by changing circulation patterns. The 19 BDCP may also reduce pyrethroid loading when land is retired from more intensive land uses 20 and restored. The effects of water operations on pyrethroids entering Delta waterways and 21 exposure to fish were analyzed in three ways. First, changes in loads of upstream pyrethroid 22 sources into the Delta were estimated by calculating median application rates of multiple 23 pesticides from Department of Pesticide Regulation (DPR) databases for each county within the 24 Sacramento and San Joaquin River watersheds and using the source water fingerprinting 25 techniques described for methylmercury to predict how much water from each watershed would 26 enter the Delta. Second, effects of water operations on changes to pyrethroid concentrations 27 from waste water treatment plants (WWTPs) were estimated using existing concentrations of 28 pyrethroids from Weston and Lydy (2010). These concentrations, in combination with discharge 29 estimates from WWTPs outside the Delta, as well as the Stockton and Sacramento WWTPs, 30 were used to compare estimated annual loads of pyrethroids entering Delta waterways with and 31 without the BDCP. Third, residence time calculations from DSM2-PTM at multiple locations 32 within the Delta were used to predict the effect of water operations on the exposure time of an 33 organism to pyrethroids within the Delta. The effect of changes in land use resulting primarily 34 from BDCP habitat restoration was analyzed by using DFG land use maps to determine acreages 35 of specific crop types on hypothetical habitat restoration sites, calculating average application 36 rates of pyrethroids on each crop type from the DPR database, and calculating total application 37 rate. Using the assumption that 0.11 percent of the pyrethroid application loads onto fields 38 enters the Sacramento and San Joaquin waterways as runoff (Werner and Oram 2008), the total 39 reduction in loads was calculated. 40



The analysis of the effects of the BDCP on changes to endocrine disrupting compound loads was 1 combined with the analysis of pyrethroids because the best available data on EDC loads to the 2 Delta consist of information on pyrethroid applications for agricultural and commercial use and 3 in wastewater treatment plant effluent. 4

While the BDCP is not a source of increased copper loading, it is expected to affect copper loads 5 as a result of four actions: water operations, nonnative aquatic vegetation control under CM9, 6 tidal habitat restoration in the Cache Slough ROA and enhanced floodplain inundation in the 7 Yolo Bypass, and changed land use. The effect of water operations were predicted using 8 existing copper concentrations and the source water fingerprinting methods described for 9 methylmercury. The effect of nonnative aquatic vegetation control on copper concentrations in 10 Delta waterways was addressed using existing application rates used by the Department of 11 Boating and Waterways for their existing nonnative plant removal programs and the acreage of 12 anticipated removal under the BDCP. Due to a paucity of information, a qualitative assessment 13 was conducted to determine the effect of restoration in Cache Slough and the Yolo Bypass, two 14 locations with large copper deposits. The effect of changes in land use on copper pesticide use 15 was analyzed identically to the analysis of pyrethroid pesticides. 16

The effect of the BDCP on ammonia/ammonium loads was estimated using the DSM2-QUAL 17 nutrient model. The analysis did not assume future changes to ammonia/ammonium loading 18 based on existing trends from WWTPs. 19

5.3.2.4 Water Quality 20

The effect of the BDCP on water temperature, dissolved oxygen concentration, turbidity, and 21 salinity in the Delta and Suisun Marsh/Bay were estimated. Effects of the BDCP on Delta-wide 22 water temperature and dissolved oxygen concentration were estimated using the DSM2-QUAL 23 nutrient model. Additional analyses were conducted to determine the effects at smaller spatial 24 scales. Effects on turbidity were assessed using the RMA turbidity model. Predicted changes in 25 salinity were estimated using the DSM2-QUAL model. 26

5.3.3 Fish Species Assessment Methods 27

This section briefly describes the methods for used for each of the analyses of covered fish 28 species. These analyses are for upstream spawning and rearing habitat (including flow and water 29 temperature), in-Delta habitat, migration flows, entrainment, in-Delta toxics and water quality, 30 predation, food availability, hatcheries, harvest, and construction. 31

5.3.3.1 Upstream Spawning and Rearing Habitat 32

Upstream spawning and rearing habitat was evaluated only for anadromous species: salmonids, 33 sturgeon, and lamprey. A number of analytical tools were available to analyze multiple 34 parameters depending on the species and the parameter. For example, the Reclamation Salmon 35 Mortality Model and SacEFT were both used to determine the effects of flows on redd 36



dewatering risk and other factors on Chinook salmon and steelhead eggs; SacEFT was used to 1 determine the effect of flows on temperature related mortality of green sturgeon eggs; available 2 literature in combination with water temperature outputs from USRWQM and the Reclamation 3 Temperature Model were used to estimate the incidence of lethal temperatures for lamprey eggs 4 and ammocoetes. Other upstream variables evaluated include spawning weighted usable area, 5 redd dewatering, redd scour, juvenile stranding, and rearing weighted usable area, primarily 6 through the use of SacEFT, SALMOD, and the Reclamation Salmon Mortality Model for 7 salmonids. Temperature and flow-related effects for larval and adult salmonids and sturgeon 8 were further evaluated using outputs from USRWQM, CALSIM, and the Reclamation 9 Temperature Model in combination with known or assumed thermal tolerances for each species. 10 Flow-related effects (redd dewatering) for lamprey were analyzed using CALSIM II and 11 USRQWM model outputs. 12

5.3.3.2 In-Delta Habitat 13

In-Delta habitat was analyzed for all lifestages of delta smelt, longfin smelt, and splittail and the 14 juvenile and adult phases of anadromous species using hypothetical restoration locations 15 developed by RMA to assist in the flow analyses. The evaluation of the effects of tidal habitat, 16 floodplain, channel margin, and riparian habitat restoration on covered fish species was mostly 17 qualitative; used DRERIP conceptual models; and focused on changes in physical habitat 18 restoration, food production, alternative migration pathways, juvenile growth rates, predation, 19 stranding, water quality, and toxics. 20

The frequency, duration, and areal extent to which the Yolo Bypass will flood as a result of the 21 BDCP was analyzed using daily flow data from CALSIM II coupled with flooded area data from 22 two-dimensional hydrodynamic modeling using MIKE-21. These results were used to assess 23 benefits of Yolo Bypass inundation to splittail spawning and juvenile rearing as well as juvenile 24 salmonid rearing. 25

The fall X2 regression model was used to estimate how BDCP water operations and habitat 26 restoration might affect the surface area of open water in the western Delta and Suisun Bay with 27 suitable salinity and turbidity for use by delta smelt. The use of this model and interpretation of 28 its results related to delta smelt habitat has been heavily debated by technical experts; no 29 consensus on the direction of the effects analysis has yet been reached. 30

5.3.3.3 Food Availability 31

Food availability is expected to change as a result of the BDCP through two primary 32 mechanisms: changes water operations and habitat restoration. The evaluation of the effects of 33 BDCP water operations on food availability was conducted primarily using the DSM2-QUAL 34 nutrient model. This model provides algal production estimates based on nutrient levels, light 35 availability, and water temperature. The effects of habitat restoration on food availability were 36 conducted using best professional judgment based on existing data within and outside the Delta. 37



The combined effect of changes to food availability to each covered fish species foraging in the 1 Delta was conducted using best professional judgment. 2

5.3.3.4 Flow 3

The BDCP may affect both downstream transport flows and upstream migration cues to 4 anadromous fish species. The evaluation of downstream transport flows in the upper rivers and 5 tributaries on salmonids, sturgeon, and lamprey used CALSIM outputs to determine flow rates in 6 multiple upstream rivers as well as multiple channels within the Delta during periods of 7 migration for each species. The Delta passage model, which uses known relationships between 8 flows in the Delta and juvenile salmon survival, was used to evaluate transport flows for 9 salmonids. The analysis of transport flows for delta and longfin smelt used daily and monthly 10 flow data from areas of known presence within the Delta and Suisun Bay during periods of 11 migration for each species. 12

The evaluation of changes to upstream migration cues on salmonids, sturgeon, and lamprey 13 compared DSM2-QUAL source water fingerprinting data between existing biological conditions 14 and under the proposed project to determine changes in flow splits at the confluence of the 15 Sacramento and San Joaquin rivers during periods of migration through the Delta for each 16 species. The evaluation also compared CALSIM II monthly flow data or USRWQM daily flow 17 data at the confluence of larger rivers to determine changes in the amount of water coming from 18 tributaries during periods of migration for each species. The effect of the BDCP on barriers to 19 migration, including the Stockton Deep Water Ship Channel, Sacramento Deep Water Ship 20 Channel, and the Yolo Bypass, were also evaluated by examining model outputs and using best 21 professional judgment. 22

The effects analysis also evaluated the change in Delta outflow/X2 in December through May as 23 an indicator of longfin smelt abundance in the DFG Fall Midwater Trawl (Kimmerer et al. 2009). 24 This evaluation of flow effects on longfin smelt abundance will be revised for the 25 January 31, 2011 draft to include the consensus among various BDCP Oversight Committee 26 technical staff that other factors, such as food availability also drive longfin smelt abundance. 27

5.3.3.5 Entrainment 28

This analysis included an evaluation of BDCP effects on four sources of entrainment: SWP/CVP 29 south Delta facilities, proposed north Delta facilities, agricultural diversions, and power plant 30 intakes. The evaluation of entrainment at south Delta facilities varied by species and, for some 31 species, by lifestage. The analysis of salmonids, sturgeon, splittail, and lamprey began with 32 calculating historical expanded salvage loss and export rates. The loss density of each species or 33 race was calculated by dividing salvage by export rate. This density was then applied to 34 predicted future monthly export rates from CALSIM II output. Entrainment of delta smelt larvae 35 and longfin smelt larvae and younger juveniles was assessed using particle tracking with a 36 number of starting positions based on historical trawl data and hydrologic conditions based on 37 DSM2-PTM scenarios. Entrainment of juvenile and adult delta smelt and older juvenile and 38



adult longfin smelt used the loss density method that were normalized by annual fall midwater 1 trawl indices for each species. A number of modifications will be made to these methods for the 2 January 31, 2011 draft Effects Analysis. In addition, other methods will be used for the 3 evaluation of some species or lifestages. 4

The evaluation of the north Delta facilities examined existing design features of screens, flow 5 and sweeping velocities, and size and shape of fish to qualitatively assess effects. 6

The evaluation of the removal of agricultural diversions due to habitat restoration and 7 construction used best professional judgment to assess effects to covered fish species. 8

The evaluation of entrainment risk on Mirant’s Pittsburg and Contra Costa power plants was 9 qualitative and utilized recent regulations to phase out completely Mirant’s once-through cooling 10 systems by 2017. 11

5.3.3.6 In-Delta toxics and water quality 12

Best professional judgment was applied to the results of the system-level analyses to estimate the 13 effects of the BDCP on toxics loads and water quality parameters in the Delta to qualitatively 14 evaluate the effects of these changed loads on covered fish species health and survival. 15

5.3.3.7 Predation 16

There are two primary ways the BDCP is expected to change predation risk: installation of north 17 Delta intakes, and CM15 Predator control. To evaluate the effects of the north Delta intakes for 18 salmonids, a striped bass bioenergetics model was developed that estimates predation rates. 19 Densities and total numbers of predators were estimated using existing density data; the zone of 20 influence (the area in which flows are altered and predators live) was estimated using best 21 professional judgment. Bioenergetics model outputs on predation rates were used by the DPM 22 and IOS to evaluate population level effects to salmonids. The effects of north Delta intakes on 23 other species were assessed by calculating estimated losses of individuals to predation. There 24 was much discussion about the assumptions and methods used for this analysis during the 25 “theme team” meetings. These issues are being resolved for the January 31, 2011 draft Effects 26 Analysis. 27

The effects of CM15 Predator Control on covered fish species were mostly evaluated 28 qualitatively. As with the evaluation of the north Delta intakes, the assumptions used for this 29 evaluation have been reconsidered and will be revised for the January 31, 2011 draft. 30

5.3.3.8 Hatcheries 31

There are two hatchery-related conservation measures in the BDCP: CM17 Hatchery and 32 Genetic Management Plans that proposes to assist DFG and USFWS in completing and 33 implementing hatchery and genetic management plans; and CM19 Conservation Hatcheries that 34



proposes to provide funding and support to conservation hatcheries for delta smelt and longfin 1 smelt. Both conservation measures were analyzed using best professional judgment. 2

5.3.3.9 Harvest 3

Best professional judgment was used to evaluate the effect of CM18 Illegal Harvest on Chinook 4 salmon, steelhead, sturgeon, and splittail. 5

5.3.3.10 Construction 6

Existing information on the techniques to be used for the construction and maintenance of the 7 five north Delta intakes was obtained. A set of best management practices (e.g., work windows, 8 protection from oil spills, use of sediment screens) was assumed based on other in-Delta 9 construction projects. Best professional judgment was used to evaluate the effects of these 10 practices on covered fish species. 11

5.3.4 Killer Whale Analysis 12

The analysis of the effects of the BDCP on southern resident killer whale was not included in the 13 August 19, 2010 draft Effects Analysis. This analysis will be completed for the January 2011 14 draft and will be based primarily on the results of the Chinook salmon evaluation because 15 Chinook salmon are a preferred prey item of the southern resident killer whale. Fecundity and 16 survival of the distinct population segment appear to be correlated with abundance of Chinook 17 salmon in inland Pacific Northwest waters (Ward et al 2009, Ford et al. 2009). Methods to be 18 used will be consistent with the NMFS Biological Opinion on the CVP and SWP (NMFS 2009). 19

5.3.5 Natural Community Assessment Methods 20

Information and analytical tools used to conduct the effects analysis on the natural communities, 21 including ecological processes, ecological gradients, native species habitat functions supported 22 by each of the natural communities as well as the extent of natural communities in the Plan Area, 23 included: 24

• Draft Chapter 2, Existing Ecological Conditions, including the BDCP GIS vegetation and 25 natural community data base; 26

• Descriptions of the BDCP conservation measures in Draft Chapter 3, Conservation 27 Strategy; 28

• The conservation implementation schedule in BDCP Chapter 6, Implementation Plan; 29

• DHCCP draft conveyance facility construction schedules; 30

• Applicable DRERIP models; 31

• Assumptions regarding development of restored and enhanced habitats (see 32 Section 5.3.1.2, Major Assumptions); 33



• Descriptions of relevant avoidance and minimization measures in Draft Chapter 3, 1 Conservation Strategy; 2

• Results of relevant modeling (e.g., modeled changes in salinity gradients); 3

• GIS data layers of conveyance facility footprints; and 4

• BDCP hypothetical footprints of restored and enhanced tidal, seasonally inundated 5 floodplain, channel margin, and riparian habitats. 6

The analysis was based on an assessment of the effects mechanisms associated with each of the 7 covered activities that could result in an adverse or beneficial effect on the natural communities. 8 Changes in the permanent, temporary, and periodic inundation effects on the extent of each 9 natural community were determined using GIS by intersecting (i.e., overlaying) the footprint 10 effect area of each of the covered activities with the GIS natural community data base layer. The 11 combined effects of constructing conveyance facilities and restoring habitats were qualitatively 12 evaluated to assess effects on habitat connectivity and movement of native wildlife species. The 13 process for calculating the extent of footprint, noise, and visual effects of implementing water 14 conveyance facility construction and habitat restoration actions on each of the natural 15 communities is illustrated in Figure 5-2. 16

Effects of covered activities on aquatic ecological processes and gradients were evaluated based 17 on results of hydrodynamic and water quality modeling and the assumptions regarding the 18 evolution of enhanced and restored tidal, channel margin, riparian, vernal pool, seasonally 19 inundated floodplain, and grassland habitats. 20



Figure 5-2. Process for Calculating Extent of BDCP Covered Activity and Conservation

Action Footprint Effects on Natural Communities and Covered Species Habitats

Discussion of Effects Analysis Chapter 5


5.3.6 Covered Wildlife and Plant Species Assessment Methods 1

Information and analytical tools used to conduct the effects analysis on covered wildlife and 2 plant species included: 3

• The BDCP covered wildlife and plant species habitat models (Appendix A, Covered 4 Species Accounts); 5

• Species information in BDCP Appendix A, Covered Species Accounts; 6

• Applicable DRERIP models; 7

• Descriptions of the BDCP conservation measures in Draft Chapter 3, Conservation 8 Strategy; 9

• The conservation implementation schedule in Draft Chapter 6, Implementation Plan; 10

• DHCCP draft conveyance facility construction schedules; 11

• Draft Chapter 2, Existing Ecological Conditions; 12

• Assumptions regarding development of restored and enhanced habitats (see Section 13 5.3.1.2, Major Assumptions); 14

• Application of relevant avoidance and minimization measures in Draft Chapter 3, 15 Conservation Strategy; 16

• Results of relevant modeling (e.g., modeled changes in salinity gradients); 17

• GIS data layers of conveyance facility footprints; and 18

• BDCP hypothetical footprints of restored and enhanced tidal, seasonally inundated 19 floodplain, channel margin, and riparian habitats. 20

The analysis was based on an assessment of the effects mechanisms associated with each of the 21 covered activities that could result in an adverse or beneficial effect on each of the covered 22 wildlife and plant species. Changes in the permanent, temporary and periodic inundation effects 23 of on the extent of each species’ habitat types were determined using GIS by intersecting the 24 footprint effect area of each covered activities with each species’ habitat model data base layers. 25 The process for calculating the extent of footprint and noise and visual effects of implementing 26 water conveyance facility construction and habitat restoration actions on covered species and 27 their habitats is illustrated in Figure 5-2. Effects of changes in salinity and hydrodynamic 28 conditions were evaluated based on results of hydrodynamic and water quality modeling and the 29 assumptions regarding the evolution of enhanced and restored tidal, channel margin, riparian, 30 vernal pool, seasonally inundated floodplain, and grassland habitats. 31

32



[Note to Reviewers: the following presents draft Section 5.4, Summary of Results, section of 1 Chapter 5, Effects Analysis, for the November 18, 2010 BDCP document. 2

Section 5.4.1 summarizes the results of the effects analysis results of covered fish species from 3 the August 19, 2010 draft for fish species and the subsequent September 9, 2010 draft enhanced 4 habitat analysis. This section is sub-divided into a description of results for each covered fish 5 species or groups of similar fish species. Where applicable, summaries of the effects on 6 population viability, designated critical habitat, and essential fish habitat are included. 7

Sections 5.4.2 and 5.4.3 summarize the effects analysis results for the natural communities and 8 covered wildlife and plant species. These two sections consist of the revised “summary of 9 effects” sections from the August 19, 2010 draft for the natural communities and species for only 10 the late long-term outcomes with full BDCP implementation. Tables presenting the extent of 11 impacts on and the level of conservation provided for each of the natural communities and 12 covered wildlife and plant species habitats at the late long-term evaluation point are provided at 13 the end of this draft.] 14

5.4 SUMMARY OF RESULTS 15

The following section summarizes the results of the August 19, 2010 draft of the BDCP effects 16 analysis and the September 9, 2010 draft enhanced habitat analysis for covered fish species. 17 Owing to the complexity and comprehensiveness of this effects analysis, there have been over 18 1,400 pages of results and over 1,900 pages of accompanying appendices generated to date. 19 Therefore, the results section presented here is a very condensed summary of the full analysis. 20 The August 19 draft effects analysis did not include a southern resident killer whale effects 21 analysis or estimated levels of take and overall syntheses and conclusions for covered fish 22 species and, therefore, are not included in this section. 23

5.4.1 Covered Fish Species 24

5.4.1.1 Delta Smelt 25

5.4.1.1.1 BDCP Effects on Stressors 26 The results of the effects analysis indicate that implementation of the BDCP conservation 27 strategy will result in a number of major changes that will reduce the impacts of stressors on the 28 delta smelt population and improve habitat conditions for larval, juvenile, and adult rearing. 29 Some adverse effects were also noted. These major findings include: 30

Expansion of habitat through physical restoration. Habitat restoration under the BDCP will 31 increase subtidal habitat extent in Suisun Marsh and West Delta ROAs by 11,000 acres in the 32 LLT. Approximately 21,000 acres of subtidal habitat will be added in the other ROAs in the 33 LLT, including 7,400 acres in the Cache Slough area, which is used extensively by delta smelt. 34



Approximately 11,000 acres will be created in the South Delta ROA, which is not used 1 extensively by delta smelt currently, but was historically. Expansion of suitable delta smelt 2 habitat to the south Delta offers the opportunity to re-establish range expansion for delta smelt, 3 geographic diversity within the Delta population, and the potential to re-establish another 4 independent spawning population of delta smelt that would be consistent with Population 5 Viability Assessment (PVA) and recovery criteria for threatened and endangered fish 6 populations. This restored habitat would provide additional spawning and rearing habitat for 7 delta smelt if these new habitat areas were to contain suitable hydraulics and water quality, and 8 was not extensively colonized by submerged aquatic vegetation or introduced predators. As 9 discussed above, the BDCP monitoring, research, and adaptive management programs will 10 address this uncertainty and provide for continual improvement in implementation design over 11 time to ensure that newly restored habitat contains suitable features for delta smelt. Specific 12 measures are included in the BDCP to control submerged aquatic vegetation and non-native 13 predators. In total, the extent of subtidal habitat in the Delta will increase by approximately 35 14 percent over existing subtidal habitat in the Delta and Suisun Marsh and Bay. 15

Increased food production. It has been postulated that food is a limiting factor for delta smelt 16 (Feyrer et al. 2007, Baxter et al. 2008, Glibert 2010, Miller unpubl. data). Changes in operations 17 and habitat restoration under the BDCP will increase hydraulic residence time in some areas of 18 the Delta, which has the potential to increase food production in those areas. In other areas, 19 residence time will decrease, which has the potential to reduce food production. The types of 20 primary producers found in the Delta water column are determined in part by the nutrient 21 composition of the water (Glibert 2010). The net near term effect of hydraulic changes is 22 therefore uncertain. 23

Habitat restoration has substantial potential to enhance food production within and adjacent to 24 restoration sites because of the substantial increase in intertidal and subtidal habitat in the ELT 25 and LLT. Delta smelt are expected to receive the greatest benefits from the creation of 26 additional habitat in the Cache Slough area. This area currently has favorable food web 27 productivity (Lehman 2010) and has supported a relatively large delta smelt population in recent 28 years. Although shallow intertidal habitat is not expected to be used by delta smelt for rearing, 29 primary production in these areas is expected to be high in the future. Adjacent subtidal areas 30 will also produce food, as well as provide delta smelt habitat as described above. The high food 31 production from intertidal marsh areas may be carried from these areas into adjacent subtidal 32 habitats that provide suitable habitat for delta smelt, increasing production there, which would 33 increase growth rates, and presumably benefit the delta smelt population. There are two schools 34 of thought regarding the amount of production expected to be exported from intertidal marsh: 35 some experts believe that export of primary production could be moderate to high whereas other 36 experts believe that exports would be low and sporadic. 37

An unknown fraction of this increased production could be consumed by the introduced overbite 38 and Asian clams. Colonization of expanded habitat areas by the Asian clam Corbula, or future 39 colonization of these habitats by non-native clams and mussels in the future, could reduce the 40



benefits of production in restored habitats. However, the BDCP Implementation Office will 1 learn from monitoring and research much more about successful and unsuccessful habitat 2 restoration design features to minimize effects of nonnative clams during the 50 year term of the 3 BDCP and will, therefore, adaptively manage restoration design to minimize these effects. 4

Changes in Fall X2. In comparison with the RPAs in the existing delta smelt biological opinion, 5 BDCP will modify the location of X2 position during fall in below normal, above normal and 6 wet water years. However, this RPA has not yet been implemented due to lack of suitable 7 hydrological circumstances. Moreover, it was not accepted by Reclamation and is under 8 contention in litigation, the outcome of which cannot be predicted here. Thus it is not currently 9 an existing condition for purposes of comparison to BDCP. In order to be conservative, 10 however, analysis has been conducted to evaluate the change in fall X2 location that would occur 11 under BDCP relative to the fall X2 RPA. 12

Under the BDCP, X2 position will move upstream in the fall months of below normal, above 13 normal and wet years relative to its location assuming “existing biological conditions (EBC)” in 14 the existing RPA. In fall, this would occur in the wettest 60 percent of years, although it would 15 not be different from the EBC under the driest 40 percent of conditions. Higher X2 position will 16 reduce the surface area of open water with salinity and turbidity levels that some consider 17 suitable habitat for delta smelt (see e.g., Feyrer et al., 2007) by 30-40 percent, assuming the 18 current Delta configuration. These changes are similar for the ELT and the LLT. When habitat 19 restoration by the BDCP is included in the evaluation of effects on X2 position (based on LLT 20 projections), the BDCP is projected to result in approximately 25 percent more habitat in the 21 western Delta and Suisun Marsh/Bay than the EBC under the driest 50 percent of years and 22 20-40 percent less habitat under wetter years. 23

There is an ongoing discussion regarding whether or not fall X2 position is an appropriate 24 indicator of delta smelt habitat and whether it is useful in predicting population responses. This 25 issue has been identified as one of the remaining issues that require further evaluation and 26 discussion amongst the scientific community. Further analysis will be completed on this issue 27 over the next few months. 28

Reduced losses of adult delta smelt at south Delta SWP/CVP facilities. While entrainment in 29 the existing project facilities has not been shown to have a population level effect, project related 30 improvements will benefit the species. Dual export facility operations will reduce adult delta 31 smelt losses at the south Delta export facilities by approximately 50 percent from existing 32 conditions. This effect is especially pronounced during the earlier months of the migration 33 season, which will protect older, larger fish that are presumed to spawn earlier and provide a 34 disproportionately greater percentage of successful recruits in any given year. Adult losses will 35 likely increase in April, but this effect is outweighed by reduced losses during December through 36 March. The reduction in adult delta smelt losses is comparable between the ELT and LLT 37 implementation periods. 38



Reduced losses of juvenile delta smelt in south Delta SWP/CVP facilities. While neither 1 entrainment in the existing project facilities, nor project related changes in hydrodynamics, has 2 ever been shown to have a population level effect; project related improvements in these areas 3 will benefit the species. Dual export facility operations will reduce juvenile delta smelt losses at 4 the south Delta export facilities by approximately 15 percent in the ELT and 26 percent in the 5 LLT relative to corresponding existing biological conditions (EBC) conditions at the SWP 6 facilities. Little difference in loss was identified between the BDCP and the EBC at the CVP 7 facilities for juvenile delta smelt. This effect will provide a benefit for delta smelt, as well, but 8 not as great as that achieved through reductions of adult losses. Losses were slightly reduced for 9 larval delta smelt, based on PTM results, but this difference was quite small (less than 3 percent 10 in many cases) and, given the high variability in the results, is not concluded to be different from 11 that under EBC. 12

Negligible entrainment risk at north Delta intakes. As a result of the state-of-the-art design 13 characteristics (i.e., 0.2 ft/sec approach velocity, screen mesh size, screen cleaning, etc.), and the 14 northern location of the proposed intake structures relative to the geographic distribution of delta 15 smelt, the risk of entrainment or impingement of all life stages of delta smelt at the north Delta 16 intakes is negligible. 17

Entrainment in non-project diversions will be marginally reduced. The removal of non-18 project diversion due to changing land use in the Delta as a result of BDCP conservation 19 measures (e.g., conversion of agricultural land use to restored natural habitat) will provide a 20 marginal benefit to reducing entrainment risk for delta smelt. 21

Entrainment in Mirant power plants will be greatly reduced. The expected transition to 22 exclusive closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 is 23 predicted to substantially reduce and avoid entrainment and impingement of delta smelt.[ 24

Changes in toxicant levels. Toxicants (e.g., pyrethroids, copper, ammonia) have been identified 25 as a potential stressor to delta smelt (Sommer et al. 2007, Baxter et al. 2008, Werner 2010). 26 Much of the research on the effects of toxicants to delta smelt is preliminary. Under the BDCP, 27 toxicant concentrations will decrease in the west Delta as a result of minor decreases in loading 28 from upstream sources, changes in hydrodynamics, and in-Delta land use changes. Results for 29 central Delta are more mixed. Because the bulk of the delta smelt population occurs in the 30 northern Delta and confluence, the net effect of the project with regard to toxicants is beneficial. 31

Removal of submerged aquatic vegetation (SAV). SAV removal is an important secondary 32 action to habitat restoration. SAV has the potential to make habitat unsuitable for delta smelt by 33 encroaching on areas used by smelt for spawning and rearing, providing habitat for introduced 34 predators, and reducing turbidity both within SAV beds and in nearby areas. Without SAV 35 removal, some portion of the intertidal and subtidal restored habitat will be colonized by SAV 36 and become unsuitable for delta smelt. This action would be beneficial to delta smelt by keeping 37 newly created habitat available for smelt. 38



Predator removal. Localized removal of predators (e.g., striped bass, largemouth bass, 1 smallmouth bass) is expected to provide only negligible benefits to delta smelt. Currently, there 2 are few studies evaluating the effect of predation on delta smelt. After further study, more 3 information regarding the importance of predation on the delta smelt population will be known, 4 and effective predator management programs can be developed. 5

Establishment of a conservation hatchery. Establishing viable refuge populations of delta 6 smelt in a conservation hatchery will provide insurance against the potential extinction of the 7 wild populations and is an important consideration, given the low numbers of wild delta smelt. It 8 also will provide a stock of fish that could be used to assess the effects of various stressors on the 9 species without impacting wild stocks. There would be more risk and uncertainty associated 10 with increasing the scale of the facility to enhance the natural population. Long-term benefits 11 would outweigh these risks if program managers develop and maintain populations whose 12 genetic diversity and fitness are comparable to those of wild populations. 13

5.4.1.1.2 BDCP Effects on Delta Smelt Designated Critical Habitat 14 The U.S. Fish and Wildlife Service has identified the important physical and biological features, 15 or primary constituent elements (PCEs), essential for the conservation of delta smelt as: 16 “…physical habitat, water, river flow, and salinity concentrations required to maintain delta 17 smelt habitat for spawning, larval and juvenile transport, rearing, and adult migration” (59 FR 18 65256). Results of the effects analysis led to the following conclusions regarding the effects of 19 BDCP actions on designated critical habitat for delta smelt spawning, larval and juvenile 20 transport, rearing and adult migration. 21

Effects on Physical Habitat. The BDCP will result in increased spawning habitat availability 22 through habitat restoration and the removal of non-native aquatic vegetation. With respect to 23 habitat restoration, it is unknown whether restored areas will provide suitable spawning 24 substrate, although there is evidence from recent BREACH III sampling suggesting that delta 25 smelt spawn in or near Liberty Island (P. Hrodey, pers. comm.). However, the projected 26 increases in intertidal and subtidal habitat are expected to result in substantial increases in the 27 availability of suitable rearing habitat. In addition to increasing spawning and rearing habitat 28 area, increased local food production and export to adjacent pelagic habitats may occur where 29 the frequency and duration of inundation would be increased relative to existing biological 30 conditions as a result of habitat restoration (Jassby and Cloern 2000, Kneib et al. 2008, 31 Opperman 2008). 32

There is uncertainty associated with the projected benefits of habitat restoration (based on delta 33 smelt use of restored areas, proximity to population sources for native vs. exotic plants and 34 animals, etc.). The biological benefits of expanded aquatic habitat will depend, in part, on the 35 location of the habitat feature with respect to the geographic distribution of the species and their 36 lifestages, compatibility of physical habitat features with species- and life-stage specific habitat 37 requirements and preferences, the specifics of the habitat design, physical processes, and 38 configuration that would serve to reduce and avoid colonization by non-native filter-feeding 39



macroinvertebrates and predatory fish. As discussed above, the design and implementation of 1 the BDCP conservation measures include specific design characteristics (e.g., habitat diversity 2 and complexity, water depths and velocities, hydraulic flushing and residence times, wind and 3 wave induced turbidity, etc.) that work in concert with phased implementation of habitat 4 restoration, coupled with integrated monitoring and evaluation, to assess habitat performance, 5 improve performance of the habitat restoration projects, and reduce uncertainty. Through careful 6 phased implementation of habitat features developed in accordance with physical and biological 7 design characteristics, the net effect is expected to be an increase in suitable physical habitat for 8 delta smelt. 9

Effects on Water. The BDCP would have little effect on water temperature relative to the 10 effects of climate change. Water temperatures will increase in the future primarily as a result of 11 climate change, and are not expected to be intensified as a result of the BDCP. In fact, during 12 small periods during summer months, tidal marsh restoration is predicted to reduce water 13 temperature in and near marshes, which would offset some of the increases due to climate 14 change. The projected reductions in contaminant concentrations in the vicinity of the confluence 15 will decrease delta smelt contaminant exposure. These changes will range from relatively minor 16 (in the NT and ELT) to substantial (in the LLT). Finally, increases in turbidity associated with 17 floodplain, channel margin, subtidal and intertidal habitat enhancement and restoration in 18 particular, will provide a benefit to delta smelt critical habitat. These benefits will accrue during 19 spawning, larval and juvenile transport, rearing, as well as adult migration. 20

Effects on River Flows. Transport flows for larval delta smelt would decrease under the 21 proposed project during the late winter and spring in the tidal reaches of the lower Sacramento 22 River downstream of the north Delta diversions. The greatest flow reductions are expected in 23 wet, above normal, and below normal hydrologic conditions. These transport flows are likely to 24 be unimportant if temperatures are suitable and food supply is sufficient to provide adequate 25 nourishment (Nobriga pers. comm.) further upstream in the lower Sacramento River, as will 26 likely be the case in wetter periods. The project will have little effect on transport flows in drier 27 years. Consequently, changes in transport flows are expected to have little to no effect on larval 28 delta smelt critical habitat. Investigation of the potential effects of changes in Sacramento River 29 flows on delta smelt is continuing. 30

River flow rates and hydrologic conditions within the Delta may have some effect on the 31 potential for larval and juvenile delta smelt to be entrained at water diversion facilities. With 32 BDCP implementation, entrainment losses of delta smelt at the north and south Delta export 33 facilities combined are projected to decrease for larval, juvenile, and adult delta smelt. The 34 reduction in entrainment risk for delta smelt reflects the combined effects of increased exports 35 from the north Delta intakes which would be located near the upstream boundary of the delta 36 smelt geographic distribution as well as reductions in south Delta diversions and an associated 37 reduction in reverse flows in Old and Middle Rivers and other south and central Delta channels. 38 Although there will be a minor adverse effect with regard to larval transport flows within the 39 tidal reach of the Sacramento River downstream of the north Delta diversions, the improvements 40



in Delta hydrologic conditions, including both reduction in Old and Middle River reverse flows 1 as well as improvements in the net downstream flow of water through the Delta and associated 2 improvements in aquatic habitat and production of food organisms within tidal habitats and Delta 3 channels, is expected to be such that no net adverse effect on critical habitat will result. The net 4 effect will be a benefit to the species. 5

Effects on Salinity (X2 Position). There is significant scientific disagreement regarding the 6 biological importance of X2 in the fall and summer. This issue has been identified as requiring 7 further research, analysis, and discussion amongst the scientific community. Further analysis 8 will be undertaken. 9

To the extent that X2 is an indicator of delta smelt distribution, it is expected that the proposed 10 habitat projects will increase the availability of physical habitat. Under the various distribution 11 scenarios based on the potential future locations of X2, delta smelt will benefit from the newly 12 restored physical habitat in the Cache Slough complex, western Delta and/or Suisun Marsh. 13

5.4.1.1.3 BDCP Effects on Delta Smelt Population Viability 14 This section addresses the population viability of delta smelt, although a formal population 15 viability analysis has not been developed. The analysis is based on the results of the effects 16 analysis and focuses on how the BDCP will affect the following criteria (based on those 17 described for salmonids): 18

• Population abundance (population size) as reflected in the numbers of adult delta smelt 19 returning the Delta to spawn; 20

• Population growth rates (productivity) as reflected in survival rates for each life stage and 21 increasing population abundance trends (positive cohort replacement); 22

• Population spatial structure (habitat and population distribution) as reflected in the 23 geographic distribution of suitable habitat, habitat heterogeneity and complexity; and 24

• Diversity (variation in behavioral and genetic traits) as reflected in diversity and 25 complexity of habitat types, variation in life history timing, and access to suitable 26 upstream spawning and rearing habitat and migration pathways. 27

Additional considerations include reducing and avoiding threats and stressors on the delta smelt 28 population associated with actions such as changes in instream flows, water diversion effects, 29 increased vulnerability to predation, and other factors. 30

Results of the BDCP effects analysis indicate that the BDCP conservation strategy and actions 31 are consistent with the principles of delta smelt recovery planning and will address many of the 32 stressors for delta smelt as identified in the Recovery Plan for the Sacramento/San Joaquin Delta 33 Native Fishes (USFWS 1996). The BDCP conservation actions are expected to result in the 34 following outcomes related to delta smelt population viability: 35



Protection and expansion of habitat will increase abundance, growth rate, spatial structure, 1 and diversity. The BDCP will contribute to increased abundance of delta smelt through 2 protection and enhancement of suitable habitat conditions in existing areas utilized by delta smelt 3 and through habitat restoration actions that increase the amount of suitable habitat available to 4 smelt and, potentially increase smelt geographic distribution. In the south Delta, which smelt 5 used historically but do so only occasionally now, conditions will be improved through 6 decreased entrainment, increased residence time, and increased San Joaquin River flow at 7 Verona. Increased residence time and reduced entrainment losses of phytoplankton, 8 zooplankton, and nutrients from the central and southern Delta are projected to result in 9 increased phytoplankton and zooplankton densities in the Delta and contribute to increased 10 turbidity, which will increase habitat value for delta smelt. These beneficial effects could be 11 reduced by increased water temperature resulting from climate change, but this effect may be 12 offset by the effects of BDCP habitat restoration actions. Overall, these factors are expected to 13 increase larval and juvenile growth and survival, contributing to increased adult abundance. 14 These increases in habitat and abundance will contribute to increased diversity within the delta 15 smelt population, increasing the resilience of the population to extinction risk and the ability to 16 adapt to a changing environment. 17

Increased habitat will enhance food availability. The expanded floodplain, tidal wetland, and 18 channel margin habitat restoration implemented as part of BDCP will provide an increase in 19 intertidal habitat of approximately 14,360 acres and an increase in subtidal habitat of 31,320 20 acres over existing habitat. These habitats will be maintained by natural processes and will offer 21 a wide range of residence times, water depths, water velocities, tidal mixing, and habitat 22 conditions. These expanded habitats will substantially contribute to improved juvenile rearing 23 by contributing to food production and availability. The expanded area and diversity of juvenile 24 delta smelt rearing habitat and adult spawning habitat resulting from the BDCP will provide a 25 broader range of habitats within the Delta for delta smelt and increased population abundance. 26 These increases in habitat and abundance will likely contribute to increased diversity within the 27 delta smelt population, increasing the resilience of the population to extinction risk and the 28 ability to adapt to a changing environment. 29

Reduction in SWP/CVP losses will increase survival. While entrainment in the existing 30 project facilities has ever been shown to have a population level effect, the BDCP will 31 substantially reduce entrainment of juvenile and adult delta smelt at south Delta facilities by 32 approximately one fourth and one half, respectively. This effect will increase survival of 33 spawners and increase recruitment of juveniles to the adult lifestage. 34

5.4.1.1.4 Overall Conclusions for Delta Smelt 35

The following overall conclusions were made based on the results of the effects analysis for delta 36 smelt. 37

Contribution to Recovery. As a comprehensive package of conservation measures, BDCP will 38 contribute to the survival and recovery of the delta smelt population through cumulative 39



reduction in stressors and improvements in habitat that together contribute to increase population 1 abundance. The BDCP conservation strategy and actions are consistent with the principles of 2 delta smelt recovery planning and will address many the stressors of delta smelt as identified in 3 the Recovery Plan for the Sacramento/San Joaquin Delta Native Fishes (USFWS 1996). Habitat 4 conditions and water operations resulting from implementation of BDCP conservation measures 5 will allow for increased individual growth and survival, and consequently, increased delta smelt 6 population abundance within the Delta. There are no actions proposed as part of BDCP that are 7 inconsistent or incompatible with long-term delta smelt recovery plan implementation. 8

Net Beneficial Effects on Designated Critical Habitat. The BDCP implementation is expected 9 to improve critical habitat for delta smelt. The PCEs for delta smelt critical habitat include 10 physical habitat, water quality and food availability, to support delta smelt spawning, larval and 11 juvenile transport, rearing habitat, and adult migration. It will result in a substantial increase in 12 available habitat area, although the utility of this habitat cannot be fully known from existing 13 information. This increase in habitat extends beyond the rearing space that delta smelt occupy 14 and incorporates areas that are likely to experience increased food production. BDCP habitat 15 restoration will likely increase turbidity, which would increase feeding success for delta smelt 16 and assist in the avoidance of predators. The proposed project will reduce the concentration of 17 toxic compounds in the areas most used by delta smelt, although changes in concentration are 18 variable. 19

Need for Adaptive Management. Due to a limitation of available analytical tools, the 20 magnitude of the effects of BDCP actions on delta smelt could not be quantified. There are a 21 number of uncertainties described in the analyses of the effects of the project on delta smelt. 22 Many of these uncertainties result from substantial scientific uncertainties regarding the factors 23 affecting current trends in species abundance, basic life history requirements, and how the Delta 24 may respond to large-scale changes in its habitat area and hydrology. To address this 25 uncertainty, the BDCP includes an extensive monitoring program to evaluate the effectiveness of 26 BDCP actions, a research program to expand the knowledge base, and an adaptive management 27 program that provides the flexibility to adjust water operations criteria for certain parameters 28 within specified adaptive ranges (see CM1 Water Facilities and Operations in Chapter 3, 29 Conservation Strategy). The habitat restoration program will be adaptively managed as habitat is 30 restored in phases over time. This phasing of restoration will provide an opportunity to learn 31 which restoration strategies work and which do not, and to employ that knowledge to subsequent 32 project planning to maximize their success. Because these monitoring, research and adaptive 33 management programs are integral components of the project, there is the opportunity and 34 flexibility to adaptively change the conservation measures, within prescribed bounds, reduce 35 uncertainty, and improve outcomes. 36



5.4.1.2 Longfin Smelt 1

5.4.1.2.1 BDCP Effects on Stressors 2 The results of the effects analysis indicate that implementation of the BDCP conservation 3 strategy will result in a number of major changes that will reduce the impacts of stressors on the 4 longfin smelt population and improve habitat conditions for larval, juvenile, and adult rearing, 5 although some adverse effects were also noted. These major findings include: 6

Expansion of habitat through physical restoration. Habitat restoration under the BDCP will 7 increase subtidal habitat extent in Suisun Marsh and West Delta ROAs by 11,000 acres in the 8 LLT , which are used extensively by longfin smelt. Approximately 11,000 acres will be created 9 in the South Delta ROA, which is not used extensively by longfin smelt currently, but was 10 historically. These restored subtidal areas may provide additional spawning and rearing habitat 11 for longfin smelt if these areas are constructed to have appropriate hydraulics and water quality, 12 and are not extensively colonized by SAV or introduced predators (BDCP includes specific 13 measures to control SAV and predators). In total, the extent of subtidal habitat in the Delta will 14 increase by approximately 35 percent over existing subtidal habitat in the Delta and Suisun 15 Marsh and Bay. 16

Increased food production. It has been postulated that food is a limiting factor for longfin 17 smelt (Baxter et al. 2008). Changes in operations and habitat restoration under the BDCP will 18 increase hydraulic residence time in some areas of the Delta, which has the potential to increase 19 food production in those areas. The types of primary producers found in the Delta water 20 column are determined, in part, by the nutrient composition of the water (Glibert 2010). The net 21 near term effect of hydraulic changes is therefore uncertain. 22

Habitat restoration has substantial potential to enhance food production within and adjacent to 23 restoration sites because of the substantial increase in intertidal and subtidal habitat in the ELT 24 and LLT. Although shallow intertidal habitat is not expected to be used by longfin smelt for 25 rearing, primary production in these areas is expected to be high in the future. Adjacent subtidal 26 areas will also produce food, as well as provide longfin smelt habitat as described above. The 27 high food production from intertidal marsh areas may be carried from these areas into adjacent 28 subtidal habitats that provide suitable habitat for longfin smelt, increasing production there, 29 which would increase growth rates, and presumably benefit the longfin smelt population. There 30 are two schools of thought regarding the amount of production expected to be exported from 31 intertidal marsh: some experts believe that export of primary production could be moderate to 32 high whereas other experts believe that exports would be low and sporadic. 33

An unknown fraction of this increased production could be consumed by the introduced overbite 34 and Asian clams. Colonization of expanded habitat areas by the Asian clam Corbula, or future 35 colonization of these habitats by non-native clams and mussels in the future, could reduce the 36 benefits of production in restored habitats. This potential effect could be off-set by concentrating 37 early habitat actions in areas like Suisun Marsh, which have not been colonized by Corbula and 38



where brackish conditions are inhospitable to freshwater SAV such as Egeria. The BDCP 1 Implementation Office will learn from monitoring and research much more about successful and 2 unsuccessful habitat restoration design features to minimize effects of nonnative clams during 3 the 50 year term of the BDCP and will, therefore, adaptively manage restoration design to 4 minimize these effects. 5

Reduced losses of longfin smelt at south Delta SWP/CVP facilities. Dual export facility 6 operations under the BDCP will reduce adult longfin smelt losses by approximately 60 percent at 7 both south Delta export facilities relative to existing biological conditions during both the ELT 8 and LLT. While adult entrainment in the south Delta project facilities has been negligible in all 9 but a few very dry years, the further reduction in proportional entrainment under the BDCP will 10 benefit the species. Dual operations will likely increase juvenile longfin smelt losses in the ELT 11 by approximately 20 percent at the south Delta SWP facility and 4-7 percent at the CVP facility. 12 In the LLT, no difference was detected in juvenile longfin smelt losses between the BDCP and 13 EBC at either facility. Dual operations will likely result in negligible reductions (less than 2 14 percent in many cases) in larval entrainment under the BDCP relative to the EBC. Based on the 15 relative magnitude of differences in predicted losses under the BDCP and the EBC for each of 16 these lifestages, and the relative importance of each lifestage to the overall population, 17 reductions in adult losses are expected to outweigh increases in entrainment projected for 18 juveniles, resulting in a net benefit to longfin smelt. 19

Negligible entrainment risk at north Delta intakes. As a result of the state-of-the-art design 20 characteristics (i.e., 0.2 ft/sec approach velocity, screen mesh size, screen cleaning, etc.), and the 21 northern location of the proposed intake structures relative to the geographic distribution of 22 longfin smelt, the risk of entrainment or impingement of all life stages of longfin smelt at the 23 north Delta intakes is negligible. 24

Entrainment in non-project diversions will be marginally reduced. The removal of non-25 project diversion due to changing land use in the Delta as a result of BDCP conservation 26 measures (e.g., conversion of agricultural land use to restored natural habitat) will provide a 27 marginal benefit to reducing entrainment risk for longfin smelt. 28

Entrainment in Mirant power plants will be greatly reduced. The expected transition to 29 exclusive closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 is 30 predicted to substantially reduce and avoid entrainment and impingement of longfin smelt. 31

Changes in Delta hydrodynamics. There is significant disagreement regarding the biological 32 importance of the location of X2. While the y-intercept of the statistical relationship between 33 Delta outflow and longfin smelt abundance reported by Kimmerer (2002) and Rosenfield and 34 Baxter (2007) has decreased in recent years, the relationship is still present (Sommer et al. 2007, 35 Rosenfield and Baxter 2007). At the same time, the response of longfin smelt abundance to 36 levels of flow has dramatically declined, with the same magnitude of flows expected to produce 37 less and less smelt over time. 38



Documented decreases in abundance between Age 1 and Age 2 fish (Rosenfeld and Baxter 2009) 1 also suggest that a population bottleneck occurs after the recruitment from larvae to juvenile, 2 suggesting that potential reductions in larval abundance based on reduced transport flows 3 occurring prior to this bottleneck may not have significant population level effects. 4

Due to the scientific uncertainty regarding how to interpret any potential changes in the location 5 of X2, this issue has been identified as requiring further research, analysis, and discussion 6 amongst the scientific community. Further analysis will be undertaken. 7

Changes in toxicant levels. Toxicants (e.g., pyrethroids, copper, ammonia) have been identified 8 as a potential stressor to longfin smelt (Sommer et al. 2007, Baxter et al. 2008, Werner 2010). 9 Although studies focusing on the effects of toxics on longfin smelt have not yet been conducted, 10 research on delta smelt should provide an indication of the magnitude of the impact on longfin 11 smelt. Much of this research, however, is preliminary. Under the BDCP, toxicant 12 concentrations will decrease in the west Delta as a result of minor decreases in loading from 13 upstream sources, changes in hydrodynamics, and in-Delta land use changes. Results for the 14 central Delta are more mixed. Because the bulk of the longfin smelt population occurs in the 15 northern Delta and confluence, the net effect of the project with regard to toxicants is beneficial. 16

Removal of submerged aquatic vegetation (SAV). SAV removal is an important secondary 17 action to habitat restoration. SAV has the potential to make habitat unsuitable for longfin smelt 18 by encroaching on areas used by smelt for spawning and rearing, providing habitat for 19 introduced predators, and reducing turbidity both within beds and in nearby areas. Without SAV 20 removal, some portion of the intertidal and subtidal restored habitat will be colonized by SAV 21 and become unsuitable for longfin smelt. This action would be beneficial to longfin smelt by 22 keeping newly created habitat available for smelt. 23

Predator removal. Localized removal of predators (e.g., striped bass, largemouth bass, 24 smallmouth bass) is expected to provide only negligible benefits to longfin smelt. Currently, 25 there are few studies evaluating the effect of predation on longfin smelt. After further study, 26 more information regarding the importance of predation on the longfin smelt population will be 27 known, and effective predator management programs can be developed. 28

Establishment of a conservation hatchery. Establishing a viable refugial population of longfin 29 smelt in a conservation hatchery will provide insurance against the potential extinction of the 30 wild population and is an important consideration, given the low numbers of wild longfin smelt. 31 It also will provide a stock of fish that could be used to assess the effects of various stressors on 32 the species without impacting the wild stock. There would be more risks and uncertainty 33 associated with increasing the scale of the facility to enhance the natural population. Long-term 34 benefits would outweigh these risks if program managers develop and maintain populations 35 whose genetic diversity and fitness are comparable to those of wild populations. 36



5.4.1.2.2 BDCP Effects on Longfin Smelt Population Viability 1 This section addresses the population viability of longfin smelt, although a formal population 2 viability analysis has not been developed. The analysis is based on the results of the effects 3 analysis and focuses on how the BDCP will affect the following criteria (based on those 4 described for salmonids): 5

• Population abundance (population size) as reflected in the numbers of adult longfin smelt 6 returning to the Delta to spawn; 7


• Population spatial structure (habitat and population distribution) as reflected in the 10 geographic distribution of suitable habitat, habitat heterogeneity and complexity; and 11

• Diversity (variation in behavioral and genetic traits) as reflected in diversity and 12 complexity of habitat types, variation in life history timing, and access to suitable 13 upstream spawning and rearing habitat and migration pathways. 14

Additional considerations include reducing and avoiding threats and stressors on the longfin 15 smelt population associated with actions such as changes in instream flows, water diversion 16 effects, increased vulnerability to predation, and other factors. 17

Results of the BDCP effects analysis show that the BDCP conservation strategy and actions are 18 consistent with the principles of longfin smelt recovery planning and will address many of the 19 stressors for longfin smelt as identified in the Recovery Plan for the Sacramento/San Joaquin 20 Delta Native Fishes (USFWS 1996). The BDCP conservation actions are expected to result in 21 the following outcomes related to longfin smelt population viability: 22

Protection and expansion of habitat will increase abundance, growth rate, spatial structure, 23 and diversity. The BDCP will contribute to increased abundance of longfin smelt through 24 protection and enhancement of suitable habitat conditions such as food availability and turbidity 25 within upstream spawning and juvenile rearing habitats, as well as contribute to an increased 26 smelt geographic distribution of adult spawning and juvenile rearing habitat within the Delta. 27 Increased access to, and extent of suitable rearing habitat, as well as increased food resources, 28 from habitat restoration will contribute to increased juvenile growth and survival, thereby 29 contributing to increased adult abundance. 30

Long-term implementation of BDCP conservation measures will reduce the adverse effects of a 31 number of current stressors and improve longfin smelt survival that will result in improved 32 population growth rates (a greater probability of maintaining positive cohort replacement) over a 33 wide range of hydrologic and environmental conditions that occur within the Central Valley. 34

Increased habitat will enhance food availability. The expanded floodplain, tidal wetland, and 35 channel margin habitat restoration implemented as part of the BDCP will provide an increase in 36



intertidal habitat of approximately 14,360 acres and an increase in subtidal habitat of 31,320 1 acres over existing habitat. These habitats will be maintained by natural processes and will offer 2 a wide range of residence times, water depths, water velocities, tidal mixing, and habitat 3 conditions. These expanded habitats will contribute to improved juvenile rearing by contributing 4 to food production and availability. The expanded area and diversity of juvenile rearing habitat 5 and adult spawning habitat resulting from the BDCP will provide a broader range of habitats 6 within the Delta for longfin smelt which is expected to contribute to increased population 7 abundance. These increases in habitat and abundance will likely contribute to increased diversity 8 within the longfin smelt population, increasing the resilience of the population to extinction risk 9 and the ability to adapt to a changing environment. 10

Reduction in SWP/CVP losses will increase survival. Adult entrainment in the south Delta 11 project facilities has been negligible in all but a few very dry years. Nevertheless, as the BDCP 12 would further reduce proportional entrainment, the species will benefit. The BDCP will reduce 13 losses of adult longfin smelt at south Delta facilities by approximately 60 percent. This effect 14 will contribute to an increased production of eggs and greater larval abundance. Losses of 15 juvenile longfin smelt will be higher by approximately 15 to 26 percent, although this increase is 16 outweighed by reduced losses to adults, due to differences in magnitude, and the relative 17 importance of adults compared to juveniles to the population (an adult has already survived to 18 the age of reproduction, whereas a juvenile has not). 19

5.4.1.2.3 Overall Conclusions for Longfin Smelt 20 The following overall conclusions were made based on the results of the effects analysis for 21 longfin smelt. 22

Contribution to Recovery. As a comprehensive package of conservation measures, BDCP will 23 contribute to the survival and recovery of the longfin smelt population through cumulative 24 reduction in stressors and improvements in habitat that together contribute to increase population 25 abundance. The BDCP conservation strategy and actions are consistent with the principles of 26 longfin smelt recovery planning and will address many the stressors of longfin smelt as identified 27 in the Recovery Plan for the Sacramento/San Joaquin Delta Native Fishes (USFWS 1996). 28 Habitat conditions and water operations resulting from implementation of BDCP conservation 29 measures will allow for increased individual growth and survival, and consequently, increased 30 longfin smelt population abundance within the Delta. There are no actions proposed as part of 31 BDCP that are inconsistent or incompatible with long-term longfin smelt recovery plan 32 implementation. 33

Need for Adaptive Management. Due to a limitation of available analytical tools, the 34 magnitude of the effects of BDCP actions on longfin smelt could not be quantified. There are a 35 number of uncertainties described in the analyses of the effects of the project on longfin smelt. 36 Many of these uncertainties result from substantial scientific uncertainties regarding the factors 37 affecting current trends in species abundance, basic life history requirements, and how the Delta 38 may respond to large-scale changes in its habitat area and hydrology. To address this 39



uncertainty, the BDCP includes an extensive monitoring program to evaluate the effectiveness of 1 BDCP actions, a research program to expand the knowledge base, and an adaptive management 2 program that provides the flexibility to adjust water operations criteria for certain parameters 3 within specified adaptive ranges (see CM1 Water Facilities and Operations in Chapter 3, 4 Conservation Strategy). The habitat restoration program will be adaptively managed as habitat is 5 restored in phases over time. This phasing of restoration will provide an opportunity to learn 6 which restoration strategies work and which do not, and to employ that knowledge to subsequent 7 project planning to maximize their success. Because these monitoring, research and adaptive 8 management programs are integral components of the project, there is the opportunity and 9 flexibility to adaptively change the conservation measures, within prescribed bounds, reduce 10 uncertainty, and potentially improve outcomes. 11

5.4.1.3 Salmonids 12

5.4.1.3.1 BDCP Effects on Stressors 13 The results of the effects analysis indicate that implementation of the BDCP conservation 14 strategy will result in a number of major changes that will reduce the impacts of stressors on the 15 Chinook salmon and Central Valley steelhead populations and improve habitat conditions for 16 juvenile rearing and migration within the Delta, and adult upstream migration to natal spawning 17 areas, although some adverse effects were also noted. These major findings include: 18

Greater access to habitats used by juvenile salmonids. BDCP conservation measures will 19 result in substantially increased access to expanded seasonal floodplain, tidal wetland, and 20 channel margin habitat, geographically distributed throughout the Delta. This restoration will 21 benefit juvenile salmon and steelhead produced in the Sacramento River Basin, east side 22 tributaries, and the San Joaquin River Basin. Intertidal habitat could be expanded by 23 approximately 6,040 acres in the near-term with an additional 7,250 acres in subtidal habitat. 24 During the early long-term intertidal habitat could be expanded by 10,990 acres and subtidal 25 habitat could be expanded by 9,350 areas. During the late long-term intertidal habitat could be 26 expanded by 14,360 acres and subtidal habitat could be expanded by 31,320 acres. The Yolo 27 Bypass floodplain rearing habitat would be enhanced by increased frequency and duration of 28 flood flows. Up to 10,000 acres of new floodplain habitat would be restored across the Delta, 29 mostly in the south Delta along the San Joaquin, Old, and Middle Rivers. 30

Among the salmonids winter-run and fall-run Chinook salmon are expected to receive the 31 greatest benefit from expanded juvenile rearing habitat within the Delta. Both of these species 32 have fry that rear within the Delta for several months before migrating into the ocean. During 33 the juvenile rearing and emigration period (late winter and spring months) these juveniles would 34 benefit from increased access to seasonally inundated floodplain habitat as well as shallow-35 water, low-velocity juvenile rearing habitat located throughout the various regions of the Delta. 36 Late fall-run and spring-run Chinook salmon and steelhead primarily rear in upstream riverine 37 habitats and typically their juveniles do not spend a prolonged period rearing within the Delta. 38 The older juveniles and smolt stages of these and other salmonids would, however, gain benefits 39



from increased availability of channel margin habitat and food production in tidally inundated 1 wetland habitat during their emigration from the Sacramento and San Joaquin River systems. 2 The increased access to suitable habitat for foraging and rearing, and the increased availability of 3 prey, are expected to contribute directly to increased growth, juvenile health, and survival. 4

Habitat benefits for Sacramento River salmonids. Major expansion in access to floodplain 5 habitat (Yolo Bypass), tidal habitat (Cache Slough complex, Suisun Marsh, West Delta ROAs), 6 and channel margin habitat (e.g., along the mainstem Sacramento River and Sutter and 7 Steamboat sloughs) will occur in the northern and western Delta, and will serve to benefit 8 juvenile steelhead, spring-run, winter-run, fall-run, and late fall-run Chinook salmon produced in 9 the Sacramento River Basin. Intertidal habitat could be expanded by approximately 2,950 acres 10 in Cache Slough in the near-term with an additional 1,210 acres in subtidal habitat. During the 11 early long-term intertidal habitat in Cache Slough could be expanded by 5,750 acres and subtidal 12 habitat could be expanded by 2,320 areas. During the late long-term intertidal habitat could be 13 expanded by 6,710 acres from existing conditions and subtidal habitat could be expanded by 14 7,400 acres. Additional substantial tidal and subtidal habitat expansion in the western Delta and 15 Suisun Marsh, and channel margin habitat enhancement on the Sacramento River (at least 5 16 miles) and on Sutter and Steamboat sloughs, would also be available on the migration pathway 17 for juvenile steelhead, winter-run, spring-run, fall-run, and late fall-run Chinook salmon. 18

Rearing habitat function for Sacramento River Basin salmonids of the existing floodplain in the 19 Yolo Bypass will be enhanced through an increase in the frequency and duration of inundation 20 with an approximately a 2- to -3 fold increase in frequency of short duration flood events (>30 21 days), as much as a 2- to 6-fold increase in frequency of intermediate duration flood events 22 (between 30-45 days), and as much as a 3- to 9-fold increase in frequency of long duration flood 23 events (>45 days). Extended rearing opportunities within the floodplain habitat have been shown 24 to result in increased growth and survival of juvenile Chinook salmon (Sommer et al. 2001). 25 Results of bioenergetic modeling suggested that feeding success was greater on the floodplain 26 than in the Sacramento River (Sommer et al. 2001). Survival rates of marked salmon were found 27 to be overall greater for those fish rearing in the floodplain, likely due to increased feeding 28 success, increased prey availability, increased seasonal water temperatures, and availability of 29 shallow-water low-velocity rearing habitat, although there was variation in the data showing 30 equal or reduced survival in some years. The factors that contributed to increased and decreased 31 juvenile survival and growth within the Yolo Bypass are continuing to be analyzed. 32

The benefits of rearing on seasonally inundated floodplain habitat within the Yolo Bypass would 33 be available for all salmonids produced in the Sacramento River watershed with the exception of 34 those from the lower American River. Rearing by juvenile winter-run, spring-run, fall-/late fall-35 run Chinook and steelhead within the floodplain and the interconnected Cache Slough tidal 36 complex also offers the opportunity for greater life history diversity, such as extended fry 37 rearing, and a wider range of ocean entry times that reduce the risk of adverse population-level 38 effects in response to poor seasonal habitat conditions. Expanding opportunities for life history 39



diversity for salmonids and other Central Valley fish is consistent with conservation principles 1 and recovery planning. 2

Habitat Benefits for Eastside Tributary salmonids. Intertidal habitat will be expanded in the 3 lower regions of the Mokelumne and Cosumnes rivers by approximately 850 acres in the near-4 term and subtidal habitat will be expanded by 1,970 acres. These expanded intertidal and 5 subtidal habitats will then continue to function during the ELT and LLT to benefit east side 6 steelhead and fall-run Chinook salmon, as well as other aquatic species. Mokelumne and 7 Cosumnes river basin salmonids will also benefit from habitat expansion in the western Delta 8 and Suisun Marsh and channel margin enhancements along distributaries of the Mokelumne and 9 Cosumnes rivers. 10

Habitat benefits for San Joaquin River salmonids. Expansion of intertidal and subtidal 11 habitat in the south Delta along the migratory pathway for juvenile steelhead and Chinook 12 salmon produced in the San Joaquin River basin will occur in the LLT. Approximately 1,850 13 acres of intertidal and 10,950 acres of subtidal habitat will be restored in the LLT. Restoration 14 floodplain habitat along the San Joaquin, Old, and Middle rivers will periodically (in years of 15 flood events) provide rearing habitat for San Joaquin River salmonids. San Joaquin River 16 salmonids will also benefit from habitat expansion in the western Delta and Suisun Marsh and 17 channel margin enhancements along the mainstem and distributaries of the San Joaquin River. 18

BDCP creates alternative migratory routes. Juvenile Sacramento River basin salmonid 19 survival will improve as a result of expanded access to seasonal floodplain within the Yolo 20 Bypass, which will provide opportunities for juvenile Chinook salmon and steelhead to access 21 alternative migration pathways that will circumvent the new north Delta intake structures as well 22 as the existing Delta Cross Channel and Georgiana Slough. This is expected to lead to improved 23 survival of Sacramento River basin juveniles. 24

BDCP creates conditions of enhanced food production, with potential to offset survival risk 25 from stranding, predation, and water quality. Expanded access to seasonal floodplain, tidal 26 wetland, and improved channel margin habitat will provide shallow water, low-velocity, habitat 27 areas with increased food production. Expanded access to suitable habitat is expected to benefit 28 juvenile salmon and steelhead rearing through access to alternative migration pathways, access 29 to improved juvenile rearing habitat, and access to increased food production, all of which are 30 collectively expected to result in increased juvenile growth rates and survival. 31

The magnitude of these benefits on the population abundance of Chinook salmon and steelhead 32 from BDCP expanded habitat has not been quantified. The potential to improve juvenile 33 salmonid rearing, and reduce risks associated with stranding, predation and exposure to potential 34 toxics and adverse water quality conditions is unknown relative to existing biological conditions. 35 Rigorous monitoring, adaptive management, and expanded habitat design serve to reduce 36 uncertainty and the risk of adverse effects resulting from habitat expansion. 37



Potential benefits to all Central Valley salmonid populations. Distributing expanded access 1 to suitable habitat for juvenile salmonid rearing throughout the Delta would offer potential net 2 biological benefits to all populations of Central Valley salmonids. 3

Potential but unquantified benefits from habitat modifications along levees. Currently, 4 habitat conditions within the Delta are characterized by large areas of riprap stabilized channel 5 margin with little shallow water or low velocity habitat for fry and juvenile rearing. Expanded 6 access to habitat areas characterized by shallow-water, low velocities, increased hydraulic 7 residence time, and increased food availability, as well as providing a wider geographic 8 distribution of diverse and complex habitats within the Delta, is consistent with salmonid 9 conservation principles and increases opportunities for a broader range of life history expression 10 including extended fry and juvenile rearing within the Delta. 11

Expanding life history diversity through expanded diverse habitat conditions is thought to 12 improve rearing and growth, increase survival, and increase the range of life histories. This 13 increased range of life histories includes varying juvenile rearing strategies and an expanded 14 range of ocean entry dates that serve to reduce the risk of adverse habitat conditions on a single 15 area of the species range (e.g., upstream habitat, or ocean conditions), which then contribute to 16 reduced population-level declines in survival and abundance. The benefits of increased access to 17 expanded habitat for fry and juvenile rearing on the population dynamics, resiliency, and 18 robustness of Central Valley salmonids exposed to a wide range of environmental conditions, 19 however, has not been quantified. 20

Reduced losses of salmonids at SWP/CVP facilities. While entrainment in the south Delta 21 project facilities has never been found to have a population level effect, the project is expected to 22 provide some benefits through reduced entrainment. Dual export facility operations would result 23 in a reduction in juvenile steelhead losses, including pre-screen losses, at the south Delta export 24 facilities by 40-60 percent relative to existing conditions. Dual export facility operations will 25 reduce juvenile winter-run Chinook salmon losses at the south Delta export facilities by 50-60 26 percent relative to existing conditions. Dual export facility operations will result in small 27 changes (a reduction of 1 percent to an increase of 12 percent) in juvenile spring-run salmon 28 entrainment and salvage losses at the south Delta export facilities relative to existing conditions. 29 The estimated reduction in fall-run Chinook salmon losses is 3-15 percent. 30

Negligible entrainment risk at north Delta intakes. As a result of the state-of-the-art design 31 characteristics (i.e., 0.2 ft/sec approach velocity, screen mesh size, screen cleaning, etc.), the risk 32 of entrainment or impingement of juvenile Sacramento River Basin salmonids at the north Delta 33 intakes is negligible. 34

Entrainment in non-project diversions will be marginally reduced. The removal of non-35 project diversions due to changing land use in the Delta as a result of BDCP conservation 36 measures (e.g., conversion of agricultural land use to restored natural habitat) will provide a 37 marginal benefit to reducing entrainment risk for juvenile steelhead and salmon. 38



Entrainment in Mirant power plants will be greatly reduced. The expected transition to 1 exclusive closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 is 2 predicted to substantially reduce and avoid entrainment and impingement of juvenile steelhead 3 and Chinook salmon. 4

Increased predation resulting from north Delta in-river intakes. The use of five in-river 5 intake structures located in the north Delta would create conditions that attract predatory fish 6 such as striped bass, and thus increase the risk of Sacramento River juvenile steelhead and 7 salmon to predation losses. No increase in predation risk is expected for salmonids produced in 8 east side tributaries or San Joaquin River basin. Actions that could reduce the predation risk 9 include reconfiguration of the intakes to an on-bank design that reduces predator habitat, 10 although additional analyses must be conducted to verify this conclusion, and implementation of 11 an aggressive and sustained local and regional predator removal and control program under CM6 12 Predator Control. 13

Improved survival of juvenile steelhead and salmon is expected from re-operation of the Delta 14 Cross Channel (DCC) gates and installation of non-physical barriers. Closure of the DCC gates 15 and installation and operation of non-physical barriers at key locations such as the confluence 16 between Georgiana Slough and the Sacramento River and at the head of Old River will serve to 17 improve survival of juvenile Sacramento River and San Joaquin River runs of steelhead and 18 salmon migrating downstream in the rivers and through the Delta. DCC gate closure in the fall 19 may also improve attraction flows, and thus improve olfactory cues, for upstream migrating adult 20 Sacramento River Basin salmonids and reduce inter-basin straying. It should be noted that the 21 effectiveness of non-physical barriers and their interaction with predators is based on limited 22 testing; thus outcomes for salmonids remain uncertain. 23

Reduced reverse flow conditions. BDCP dual facility operations will result in substantial 24 improvements in Old and Middle River (OMR) reverse flows within the south and central Delta 25 and a net improvement in downstream flows through the Delta, particularly from the San 26 Joaquin, Mokelumne, and Consumes river systems. These improvements in Delta 27 hydrodynamics are expected to result in improvements in habitat conditions for juvenile 28 steelhead and salmon rearing and survival during emigration. 29

No adverse upstream impacts of BDCP operations measures on steelhead, winter-run, fall-30 run, and late fall-run salmon. No major adverse effects were detected on upstream habitat 31 conditions (e.g., reservoir storage, instream flows, and water temperatures during egg incubation) 32 for steelhead, winter-run, fall-run, and late fall-run Chinook salmon in the Sacramento, Feather, 33 and American rivers. Small positive and negative changes were detected in the Sacramento and 34 Feather rivers, such as reduced summer and fall flows in the Sacramento River relative to 35 existing conditions. None of these changes would be expected to have a substantial effect on 36 salmonid life history (i.e., migration, spawning, and juvenile rearing). No changes in habitat 37 (i.e., instream flows and seasonal water temperatures) were detected in other rivers including the 38 Trinity, San Joaquin, and Stanislaus or Clear Creek. BDCP operations would have no effect on 39



habitat in non-CVP/SWP rivers including the Mokelumne, Consumes, Tuolumne, and Merced 1 rivers, or Deer, Mill, Butte, Battle, and other tributary creeks. 2

Uncertainty regarding potential egg mortality for Sacramento River spring-run salmon. 3 Results of egg mortality estimates for spring-run Chinook salmon on the Sacramento River 4 downstream of Keswick Dam showed an increase in egg mortality of approximately 5 percent 5 during early long term and 10 percent during late long term under BDCP operations in wet, 6 above normal, and below normal water years relative to existing conditions. Refinement in 7 reservoir operations and coldwater pool management may reduce this effect, but potential 8 operational changes have not been evaluated using the hydrologic and water temperature 9 simulation models. Spring-run Chinook salmon primarily inhabit tributaries to the Sacramento 10 River, such as Clear Creek, Butte Creek, Mill Creek, Deer Creek, and others. Therefore, the 11 effects of increased egg mortality on the Sacramento River would potentially adversely affect 12 only a small proportion of the spring-run Chinook salmon spawning in the Sacramento River 13 Basin. Results of the effects analysis detected no BDCP-related adverse effects to upstream 14 habitat conditions (e.g., instream flows, water temperatures during egg incubation) for spring-run 15 Chinook salmon in the Trinity River, Clear Creek, or Feather River low flow channel. BDCP 16 operations will have no effect on instream flows, temperatures, or other habitat conditions 17 affecting spring-run Chinook salmon spawning or egg incubation in other Sacramento River 18 tributaries such as Mill, Butte, Deer, or Battle Creeks. 19

Spring-run Chinook salmon are sensitive to drought and climate change. Spring-run Chinook 20 salmon egg mortality in the mainstem Sacramento River is extremely sensitive to effects of dry 21 and critically dry hydrologic conditions and future climate change. Increased egg mortality 22 under these conditions reflects natural seasonal and inter-annual variation in rivers flows, 23 coldwater storage, and temperature effects on incubating eggs that were independent of BDCP 24 operations. 25

Due to the scientific uncertainty regarding the nature and magnitude of this effect, particularly 26 after mitigation, this issue has been identified as requiring additional analysis. Further review 27 will be undertaken. 28

Uncertain effects related to operation of north Delta intake. Sacramento River flows 29 downstream of the north Delta intakes will be reduced under BDCP operations relative to 30 existing conditions. Flows will be reduced less during the winter than during the other seasons. 31 Flows will be reduced most in the wetter years. The effects of flow reduction within the lower 32 reach of the Sacramento River on the attraction and olfactory cues for upstream migrating adult 33 salmonids and survival of downstream migrating juvenile salmonids are uncertain. Flows in the 34 lower Sacramento River are influenced by tidal hydrodynamics, which also affect adult salmonid 35 attraction and juvenile migration. Increased flows in drier years offer a benefit of increased 36 attraction and olfactory cues that will contribute to reduced adult straying among watersheds. 37



Interannual and long-term hydrologic changes occur with or without BDCP operations. 1 The greatest changes in habitat conditions result from natural variation in inter-annual hydrology 2 (e.g., between wet and dry years) and future climate changes. These major effects on habitat 3 were largely independent of differences between existing conditions and BDCP operations. 4 Spring-run Chinook salmon were found to have the greatest risk among the salmonids of high 5 egg mortality resulting from exposure to elevated water temperatures, particularly in critically 6 dry water years, because of the effects of projected climate change independently, whether from 7 existing conditions or conditions with BDCP implementation; 8

Net benefits of other stressor conservation measures. Collectively, other stressor 9 conservation measures provide additional benefits to salmonids relative to existing conditions. 10 Benefits of conservation actions such as removing structures that create habitat for and attract 11 predators, reducing illegal harvest, and implementing hatchery and genetic management plans, 12 although small, contribute to the cumulative biological benefits to salmonids of BDCP. 13

5.4.1.3.2 BDCP Effects on Salmonid Designated Critical Habitat 14 Critical habitat for salmonids was designated in 2005 for Sacramento River winter-run Chinook 15 salmon, Central Valley spring-run Chinook salmon, and the distinct population segment of 16 Central Valley steelhead (70FR170: 52488-52627). Habitat for these species is further 17 characterized in the Federal Register Final Rule for each listed species (steelhead: 70 FR 52488; 18 winter-run Chinook: 58 FR 33212; Spring-run Chinook: 70 FR 52488). The effects analysis for 19 salmonids addressed how changes in SWP and CVP water operations and other BDCP 20 conservation actions would affect, beneficially or adversely, the primary constituent elements 21 (PCEs) of steelhead and Chinook salmon critical habitat.7 The PCEs used in the effects analysis 22 were: 23

• Freshwater spawning sites (i.e., providing suitable water temperatures and instream flows 24 for successful spawning in the upstream reaches of the tributary rivers); 25

• Freshwater rearing sites (i.e., providing suitable water quality for juvenile rearing, 26 instream flows to support physical habitat, connectivity with floodplains, tidal habitat, 27 channel margin habitat, and other juvenile rearing areas, and providing suitable food 28 resources for juvenile rearing); 29

• Freshwater migration corridors (i.e., reducing and avoiding passage barriers and 30 impediments, providing suitable water quality and instream flows to support access and 31 connectivity for migration within the tributary rivers, seasonally inundated floodplains 32 and tidal habitats, and migration pathways through the Delta); 33

• Estuarine areas (i.e., providing unobstructed migration and rearing opportunities, suitable 34 water quality with salinity conditions that support juvenile and adult physiological 35

7 Other important habitats for salmonids include nearshore and offshore marine coastal habitats, which will not be affected by BDCP conservation actions.



transitions between freshwater and saltwater, and providing food resources to support 1 juvenile growth and survival). 2

The effects analysis examined, through hydrologic and water quality simulation modeling, 3 predicted changes in habitat conditions that would potentially affect the quality and availability 4 of suitable habitat for each of the freshwater lifestages of Chinook salmon and steelhead. 5

Effects on Freshwater Spawning Sites. Although minor adverse and beneficial changes in 6 habitat conditions (instream flow, water temperature, and the risk of redd dewatering) were 7 detected for salmonid spawning and egg incubation in some locations, these changes will not 8 have a substantive effect on habitat conditions for steelhead or winter-run Chinook salmon. 9 Based on results of the egg mortality analysis for spring-run Chinook salmon in the mainstem 10 Sacramento River, additional analyses are underway to assess the significance of increased egg 11 mortality on spring-run salmon population dynamics, recognizing that only a small fraction of 12 the population spawns in the Sacramento River, and potential refinements to Shasta Reservoir 13 operations to reduce adverse effects. For a majority of the Central Valley rivers there was no 14 effect of the BDCP on habitat conditions for spawning relative to the EBC. The greatest 15 observed changes in habitat quality or availability are in response to interannual variation in 16 Central Valley hydrologic conditions (e.g., wet years and dry years) and in response to long-term 17 changes in Central Valley climate. Therefore, the BDCP would not affect critical habitat or the 18 success of steelhead and Chinook salmon spawning within Central Valley rivers. 19

Effects on Freshwater Rearing Sites. Although minor adverse and beneficial changes in 20 habitat conditions (flow and water temperature) were detected for salmonid rearing in some 21 locations, these changes will not have a substantive effect on habitat conditions for Chinook 22 salmon or steelhead. For a majority of the Central Valley rivers, there was no effect of the 23 BDCP on habitat conditions for juvenile rearing relative to the EBC. The greatest observed 24 changes in habitat quality or availability are in response to interannual variation in Central 25 Valley hydrologic conditions (e.g., wet years and dry years) and in response to long-term 26 changes in Central Valley climate. 27

Restoration of additional floodplain, tidal, and channel margin habitat that is geographically 28 distributed throughout the Delta will provide substantial benefits to all Central Valley salmonids. 29 The predicted magnitude of these benefits to increased juvenile growth and survival, and the 30 contribution of these conservation measures to increased adult salmonid abundance have not 31 been quantified, although positive trends towards recovery are anticipated based on salmonid 32 recovery plans. Floodplain enhancement actions designed to increase the frequency and duration 33 of access for juvenile Sacramento River basin Chinook salmon and steelhead to seasonally 34 inundated floodplain habitat in Yolo Bypass will be a significant environmental benefit of 35 BDCP. Similarly, the BDCP will substantially increase the availability of, and access to, shallow 36 water, low velocity tidal and channel margin habitat that is geographically distributed along the 37 Sacramento River and within the eastern and southern Delta and Suisun Marsh, which will 38 increase rearing habitat for juvenile Chinook salmon and steelhead from all Central Valley rivers 39



relative to existing conditions. The increased tidal and seasonal floodplain habitat proposed 1 under BDCP will contribute to improved ecological functions related to increased food 2 production and availability of prey for juvenile salmon and steelhead. Uncertainty in expanded 3 habitat performance and ecological functions will be addressed through a rigorous monitoring, 4 research, and adaptive management programs. 5

Overall, BDCP will not adversely modify habitat conditions for freshwater rearing in upstream 6 habitats within rivers tributary to the Delta. Instead, BDCP conservation actions will improve 7 habitat access, quality, and availability for juvenile Chinook salmon and steelhead rearing within 8 the lower reaches of the Sacramento and San Joaquin rivers and within the Delta and Suisun 9 Marsh. Implementation of BDCP conservation measures will contribute to a substantial increase 10 in suitable habitat for juvenile Chinook salmon and steelhead rearing. 11

Effects on Freshwater Migration Corridors. The BDCP conservation strategy includes 12 measures specifically designed to improve migratory corridors and reduce the effects of 13 obstructions that impede salmonid passage under existing conditions. Proposed actions include 14 increasing fish passage opportunities for juvenile salmon and steelhead migration into the 15 seasonally inundated Yolo Bypass floodplain, improving passage at the Fremont Weir, using 16 non-physical barriers to guide downstream migrating salmon and steelhead, improving dissolved 17 oxygen concentrations in the lower San Joaquin River, and modifying operation of the Suisun 18 Marsh Salinity Control Structure to improve fish passage. Operations under BDCP will also 19 improve hydrologic conditions as reflected by an increase in positive flows in Old and Middle 20 Rivers, as well as maintenance of instream flows within the tributaries to the Delta. These 21 conditions are intended to improve the survival of juvenile Chinook salmon and steelhead 22 migrating downstream through the Delta, in part by reducing their vulnerability to entrainment 23 losses at the existing south Delta water export facilities. Implementation of additional floodplain 24 and tidal habitat has been identified as being beneficial for all Central Valley salmonids. There 25 is a high degree of uncertainty, however, in the quantification of the magnitude of net benefits to 26 the salmonid populations, although positive trends towards recovery are anticipated based on 27 salmonid recovery plans. Reductions in instream flow in the lower reaches of the Sacramento 28 River have the potential to reduce olfactory cues and attraction flows for upstream migrating 29 adult Chinook salmon and steelhead, and river flows for downstream migrating juveniles in the 30 reach downstream of Walnut Grove. Upstream of the north Delta intakes, river flows are similar 31 between the BDCP and existing conditions. In the downstream estuarine region of the Delta, 32 tidal flows are dominant. No information is available to quantitatively assess the potential 33 effects of local flow reductions on migration and survival of Chinook salmon or steelhead. 34

Construction of five north Delta intake structures would modify local hydrodynamic conditions 35 as well as obstruct a portion of the river channel by the footprint of each intake structure. These 36 effects of the north Delta intakes would occur whether or not the intake is actually diverting 37 water. Although these physical structures and their effects on local instream flow patterns and 38 turbulence would adversely affect critical and essential habitat for salmonids in the lower reaches 39 of the Sacramento River, these effects are expected to be localized and relatively small in 40



comparison to the large areas of subtidal and intertidal aquatic habitat that would be restored and 1 available for salmonid foraging, rearing, and migration. 2

Overall, the BDCP will not adversely affect habitat conditions for Chinook salmon or steelhead 3 in migration corridors within the tributaries of the Delta and would improve passage conditions 4 for salmonids migrating through the Delta. BDCP conservation actions will reduce obstructions 5 to salmon and steelhead passage within the lower reaches of the Sacramento and San Joaquin 6 rivers and within the Delta and Suisun Marsh. Implementation of BDCP conservation measures 7 is expected to contribute to an increase in habitat conditions for juvenile Chinook salmon and 8 steelhead migration. 9

Effects on Estuarine Areas. The BDCP conservation strategy will contribute to a substantial 10 increase in access to suitable juvenile salmonid rearing habitat within the estuarine regions of the 11 Delta through channel margin habitat enhancements in the western Delta, as well as substantial 12 increases in aquatic habitat within Suisun Marsh adjacent to Suisun Bay (approximately 24,570 13 acres in the LLT). The increased access of shallow water, lower velocity juvenile rearing habitat 14 within the estuarine region of the Delta will contribute to an increase in ecological functions of 15 aquatic habitat including increased habitat diversity and complexity, foraging habitat and food 16 resources for migrating juvenile Chinook salmon and steelhead. Implementation of additional 17 tidal habitat will be beneficial to salmonids. Although positive trends towards recovery are 18 anticipated based on salmonid recovery plans, there is a high degree of uncertainty in the 19 magnitude of net population level benefits to the salmonid populations. 20

Operations under BDCP will also improve hydrologic conditions as reflected by an increase in 21 positive flows in Old and Middle rivers and maintenance of instream flows within the rivers 22 tributary to the Delta. These conditions will improve the survival of juvenile Chinook salmon 23 and steelhead migrating downstream through the Delta and improve estuarine rearing habitat 24 conditions. These improvements will benefit juvenile salmon and steelhead by providing a 25 potential for increased growth, which should contribute to increased survival. Improvements in 26 central Delta habitat and hydrodynamics will provide the greatest benefits for salmon and 27 steelhead produced in the Mokelumne, Cosumnes, and San Joaquin river basins. 28

Operations under BDCP during the late winter and spring months when juvenile salmon and 29 steelhead are migrating downstream through the estuarine region of the Delta provide outflow 30 and salinity conditions that are comparable to those under existing conditions. 31

Overall, the BDCP will not adversely affect habitat conditions for Chinook salmon and steelhead 32 within the estuarine region of the Delta. BDCP conservation actions will reduce obstructions to 33 salmon and steelhead passage within Suisun Marsh. The BDCP will contribute to an increase in 34 habitat for juvenile Chinook salmon and steelhead migration within the estuarine region of the 35 Delta. 36



5.4.1.3.3 BDCP Effects on Essential Fish Habitat for Pacific Salmon 1 The Bay-Delta system has been identified as Essential Fish Habitat (EFH) under the Magnuson-2 Stevens Act for several groups of fish species including Pacific salmon, Coastal Pelagic Species, 3 and West Coast Groundfish. EFH includes those waters and substrate necessary for fish 4 production needed to support a long-term sustainable fishery and contributions to a healthy 5 ecosystem. The BDCP effects analysis included an assessment of EFH for Pacific salmon which 6 includes winter-run, spring-run, fall-run, and late fall-run Chinook salmon from all Central 7 Valley river systems. 8

The BDCP conservation measures and operations will result in localized temporary effects on 9 EFH. These effects would be reduced through implementation of BMPs during construction and 10 other actions. The BDCP actions would result in small changes in local habitat conditions in 11 some areas of the upstream rivers and Delta, but would also result in improvements in aquatic 12 habitat conditions through changes in local hydrodynamics such as reductions in Old and Middle 13 River reverse flows and significant expansion of aquatic habitat within a variety of regions 14 distributed throughout the Delta and within Suisun Marsh. Operations will not result in 15 substantial or detectable changes in habitat conditions for EFH species inhabiting regions of the 16 Bay-Delta downstream of Suisun Bay. Based on these factors, it was concluded that 17 implementation of BDCP will not result in adverse effects to EFH that would impact Chinook 18 salmon at a population level. Instead, many of the proposed conservation actions will contribute 19 to enhanced EFH conditions within the Delta. 20

5.4.1.3.4 BDCP Effects on Salmonid Population Viability 21 The long-term recovery of Central Valley Chinook salmon and steelhead is measured by four 22 fundamental viable salmonid population (VSP) criteria as described in the NMFS (2009) draft 23 Central Valley salmonid recovery plan and Lindley et al. (2007): 24

• Population abundance (population size) as reflected in the numbers of adult Chinook 25 salmon and steelhead returning to Central Valley rivers to spawn; 26


• Population spatial structure (habitat and population distribution) as reflected in the 29 geographic distribution of suitable habitat, habitat heterogeneity and complexity, 30 abundance of juvenile smolts produced in different watersheds, and dispersal of distinct 31 population segments among watersheds; and 32

• Diversity (variation in behavioral and genetic traits) as reflected in diversity and 33 complexity of habitat types, reduced percentage of hatchery produced Chinook salmon 34 and steelhead, variation in life history and run timing, and access to suitable upstream 35 spawning and rearing habitat and migration pathways. 36



Additional considerations include reducing and avoiding threats and stressors on the populations 1 associated with actions such as changes in instream flows, water diversion effects, increased 2 vulnerability to predation, and other factors. 3

Results of the BDCP effects analysis indicate that changes predicted to occur as a direct result of 4 implementation of the conservation strategy are consistent with the principles of recovery 5 planning for Central Valley salmonids. The BDCP conservation actions will contribute to 6 recovery for salmonids because they will result in the following: 7

Restoration of habitat will increase abundance, growth rate, spatial structure, and 8 diversity. The BDCP will contribute to increased abundance of Central Valley Chinook salmon 9 and steelhead through protection and enhancement of suitable habitat conditions such as instream 10 flows and water temperatures within the upstream spawning and juvenile rearing habitats, as well 11 as contribute to increased geographically distributed and complex juvenile rearing habitat within 12 the Delta. Increased access to expanded seasonal floodplain, tidal wetlands, and improved 13 channel margin habitat will contribute to increased juvenile growth and survival, thereby 14 improving survival and contributing to increased adult abundance. Long term implementation of 15 BDCP conservation measures will reduce the adverse effects of a number of current stressors and 16 improve juvenile and adult Chinook salmon and steelhead survival that will result in improved 17 population growth rates (a greater probability of maintaining positive cohort replacement) over a 18 wide range of hydrologic and environmental conditions that occur within the Central Valley. 19

Salmonid independent populations. Conservation measures included as part of BDCP would 20 not result in the expansion of winter-run or spring-run Chinook salmon or Central Valley 21 steelhead populations into additional upstream habitats or result in the formation of additional 22 independent spawning populations. Habitat conditions and water operations within the 23 Sacramento River and Delta, however, would be complementary to the formation of additional 24 winter-run or spring-run Chinook salmon or steelhead populations within the Central Valley if 25 that should occur in the future. 26

Reduction in SWP/CVP losses will increase survival. While entrainment in the south Delta 27 SWP and CVP project facilities has never been determined to have a population level effect, 28 reduced entrainment would provide some increases in survival thereby benefiting the species. 29 Reduction in south Delta SWP and CVP exports through dual facility operations would 30 contribute to: (1) increased juvenile winter-run and fall-run Chinook salmon and steelhead 31 survival through a reduction in losses resulting from reductions in south Delta SWP and CVP 32 export operations; (2) increased juvenile rearing habitat and survival, particularly for juvenile 33 Chinook salmon and steelhead produced in the San Joaquin, Mokelumne, and Consumes river 34 watersheds as a result of reductions in Old and Middle river reverse flows and associated 35 increases in net downstream flows through the Delta; and (3) reduced risk of indirect mortality 36 for juvenile salmonids migrating through the Delta and improvements in net downstream flows 37 through the Delta channels. Actions such as expanded closure times of the Delta Cross Channel 38 gates and installation and operation of non-physical barriers at key locations (Georgiana Slough, 39



head of Old River) will further contribute to increased juvenile survival, improved attraction, and 1 reduced straying for adult Chinook salmon and steelhead returning to the San Joaquin River 2 system and east side tributaries. 3

5.4.1.3.5 Overall Conclusions for Chinook Salmon and Steelhead 4 The following overall conclusions were made based on the results of the effects analysis for 5 Chinook salmon and steelhead. 6

Net Beneficial Effects on San Joaquin River Salmonids. Steelhead, fall-run Chinook, and 7 future re-introduced spring-run Chinook salmon runs in the San Joaquin River Basin would 8 benefit from BDCP implementation by a reduction in south Delta exports and the associated 9 reduced risk of entrainment at the export facilities, reduction in the magnitude of Old and Middle 10 rivers reverse flows and improvement in the net downstream flow of water from the San Joaquin 11 River through the Delta. Reduction in potential indirect effects on the survival of juvenile 12 salmonids. Expansion of aquatic habitat in the south Delta in the LLT and habitat expansion in 13 the west Delta and Suisun Marsh in the ELT and LLT will provide opportunities for juvenile 14 salmonids emigrating from the San Joaquin River system to rear and contribute to increased 15 juvenile growth rates and survival. BDCP would have no effect on instream flows, water 16 temperatures, or other habitat conditions within the mainstem San Joaquin River or its tributaries 17 relative to existing biological conditions. Increased flow from the San Joaquin River passing 18 through the Delta will improve adult salmonid attraction and olfactory cues and contribute to 19 improved survival of emigrating juveniles. Application of a non-physical barrier at the head of 20 Old River and the effects of reductions in other stressors would contribute to the cumulative 21 benefits of BDCP conservation measures on the growth, survival, and abundance of San Joaquin 22 River salmonids. 23

Net Beneficial Effects on Mokelumne and Cosumnes River Salmonids. Steelhead and fall-24 run Chinook runs in the Mokelumne and Cosumnes rivers would benefit under BDCP by a 25 reduction in south Delta exports and the associated risk of entrainment at the export facilities, 26 reduction in the magnitude of Old and Middle River reverse flows and improvement in the net 27 downstream flow of water from the Mokelumne and Cosumnes rivers through the Delta. 28 Expansion of aquatic habitat in the lower reaches of the Mokelumne and Cosumnes rivers and 29 habitat expansion in the west Delta and Suisun Marsh would provide opportunities for juvenile 30 salmonids emigrating from the Mokelumne and Cosumnes rivers to rear and contribute to 31 increased juvenile growth rates and survival. BDCP would have no effect on instream flows, 32 water temperatures, or other habitat conditions within either the Mokelumne or Cosumnes rivers 33 relative to existing biological conditions. Closure of the Delta Cross Channel gates during the 34 fall would potentially improve attraction to the Mokelumne and Cosumnes rivers and reduce 35 straying to other Central Valley rivers. The effects of reductions in other stressors would 36 contribute to the cumulative benefits of BDCP conservation measures on the growth, survival, 37 and abundance of steelhead and fall-run Chinook salmon produced in the two rivers. 38



Net Beneficial Effects on Sacramento River Salmonids. Steelhead, winter-run, spring-run, 1 fall-run and late fall-run Chinook runs in the Sacramento River Basin would benefit from BDCP 2 implementation by a reduction in south Delta exports and the associated risk of entrainment at 3 the export facilities. Diversions from the north Delta would make use of state-of-the-art positive 4 barrier fish screens designed and operated to avoid entrainment and impingement of juvenile 5 salmonids. An increased risk of predation associated with the north Delta intake structures was 6 identified in the effects analysis, but can be substantially reduced by intake re-design in 7 combination with predator management. Reduction in the magnitude of Old and Middle rivers 8 reverse flows and improvement in Delta habitat available for juvenile salmonid rearing will 9 provide an improvement in hydrologic conditions affecting habitat and survival of juvenile 10 salmonids in the central and south Delta. Reduction in reverse flows and reductions in south 11 Delta exports results in a reduction in potential indirect effects on the survival of juvenile 12 salmonids. Expansion of aquatic habitat in the north Delta through substantial increases in the 13 frequency and duration of access to expanded seasonal floodplain rearing habitat within the Yolo 14 Bypass, that is interconnected to substantially increased tidal habitat within the Cache Slough 15 complex, will increase juvenile growth and survival, contribute to increased habitat diversity and 16 complexity, and provide opportunities for expanded diversity of life history characteristics. In 17 combination, these changes would result in greater juvenile survival and increased adult 18 salmonid abundance. Habitat expansion in the west Delta and Suisun Marsh would provide 19 opportunities for juvenile salmonids emigrating from the Sacramento River and its tributaries to 20 rear and contribute to increased juvenile growth rates and survival. BDCP would have no effect 21 on instream flows, water temperatures, or other habitat conditions in many of the Sacramento 22 River tributaries. Relatively small beneficial and adverse changes in upstream habitat within the 23 mainstem Sacramento River and Feather River were identified. Refinements in Shasta Reservoir 24 operations may help reduce a projected increase in spring-run Chinook salmon egg mortality in 25 wetter years in the mainstem Sacramento River. Reduced flows in the lower reach of the 26 Sacramento River downstream of the north Delta intakes in wetter years may affect adult 27 salmonid attraction and juvenile survival, however, the potential for adverse effects within the 28 tidal reach of the river are uncertain. Installation of a non-physical barrier at Georgiana Slough 29 and the effects of reductions in other stressors would contribute to the cumulative benefits of 30 BDCP conservation measures on the growth, survival, and abundance of Sacramento River 31 salmonids. 32

Contribution to Recovery. BDCP conservation measures are consistent with and 33 complementary to salmonid recovery within the Central Valley as identified in the NMFS draft 34 recovery plan (NMFS 2009). BDCP conservation measures would not result in the 35 establishment of new independent salmonid populations within the Central Valley. Habitat 36 conditions and water operations within the Sacramento River and Delta would, however, be 37 complementary to the formation of additional winter-run or spring-run Chinook salmon or 38 steelhead populations within the Central Valley if that should occur in the future. There are no 39 actions proposed as part of BDCP that are inconsistent or incompatible with long-term salmonid 40 recovery plan implementation. 41



Net Beneficial Effects on Designated Critical Habitat. BDCP conservation actions would 1 contribute substantially to improved habitat availability and diversity that would benefit juvenile 2 salmonids and reduce stressors that currently adversely affect Chinook salmon and steelhead 3 growth, survival, and population abundance. Substantial reductions in Old and Middle River 4 reverse flows and expanded intertidal, subtidal, and seasonal floodplain habitat represent major 5 contributions toward improved critical habitat for winter-run and spring-run Chinook salmon and 6 steelhead within the Delta. These improvements in critical habitat conditions for listed 7 salmonids would contribute to increased juvenile growth and survival, greater life history and 8 habitat diversity, and are expected to result in increased adult salmonid abundance. Effects of 9 BDCP operations on critical habitat upstream of the Delta has been evaluated and results show 10 relatively small adverse and beneficial effects on habitat conditions for spawning and juvenile 11 rearing on the mainstem Sacramento River and Feather River, but no incremental changes in 12 habitat conditions on other Central Valley river systems. The magnitude of beneficial effects 13 associated with changes in water operations, expanded aquatic habitat, improved hydrologic 14 conditions within the Delta, and reduction in other stressors have not been quantified. 15 Uncertainties regarding the ecological functions and net biological response of salmonids to 16 expanded diverse habitats geographically distributed in various regions of the Delta, and changes 17 in water operations and hydrologic conditions within the rivers and Delta will be addressed 18 through the BDCP monitoring, research, and adaptive management programs. 19

Net Beneficial Effects on Essential Fish Habitat. Based on results of the effects analysis it 20 was concluded that implementation of BDCP conservation measures and operations would result 21 in localized temporary effects on EFH. These effects would be reduced through implementation 22 of BMPs during facilities construction and other actions. The BDCP actions would result in 23 small changes in local habitat conditions in some areas of the upstream rivers and Delta but 24 would also result in substantial improvements in aquatic habitat conditions through changes in 25 local hydrodynamics such as reductions in Old and Middle River reverse flows and significant 26 expansion of aquatic habitat within a variety of regions distributed throughout the Delta and 27 within Suisun Marsh as a result of BDCP habitat restoration actions. Operations would not be 28 expected to result in substantial or detectable changes in habitat conditions for EFH species 29 inhabiting regions downstream of Suisun Bay. Based on these factors, it was concluded that 30 implementation of BDCP would not result in adverse effects to EFH that would impact species at 31 a population level and that many of the proposed conservation actions would contribute to 32 enhanced EFH conditions within the Delta. 33

Need for Adaptive Management. As a comprehensive package of conservation measures, 34 BDCP will contribute to the survival and recovery of Central Valley Chinook salmon and 35 steelhead populations through cumulative reduction in stressors and improvements in habitat that 36 together contribute to increase population abundance. The magnitude of the effects of BDCP 37 actions on Chinook salmon and steelhead recovery, however, has not been quantified. There 38 remain areas of uncertainty regarding the effectiveness of various individual conservation actions 39 that will be addressed as part of BDCP implementation through the BDCP monitoring, research, 40 and adaptive management programs. 41



5.4.1.4 Sacramento Splittail 1

5.4.1.4.1 BDCP Effects on Stressors 2 Based on results of the effects analysis, the BDCP will produce a number of major changes 3 within the Delta that will reduce the impacts of ecological stressors on the Sacramento splittail 4 population and improve habitat conditions for adult reproduction and larval and juvenile rearing. 5 These major effects analysis findings include: 6

Increased Yolo Bypass inundation creates more spawning and rearing habitat. Limited 7 availability of spawning habitat and rearing habitat for the larval and early juvenile life stages is 8 a primary stressor on the splittail population, especially in dry years when floodplains are not 9 inundated. Implementation of CM2, Yolo Bypass Fishery Enhancement, will increase the 10 frequency and duration of Yolo Bypass inundation, resulting in substantial increases in spawning 11 and rearing habitat availability. The increased duration of flooding events will reduce the risk of 12 stranding. Rates of predation on splittail larvae will not be affected by CM2. Increases in 13 habitat surface area are predicted to be especially large (on a percentage basis) in dry years, 14 when Sacramento River flow is low. Predicted habitat increases are somewhat larger with the 15 combined effects of the proposed project and climate change in the ELT and LLT. There is 16 some uncertainty regarding the level of flow from the Bypass that is sufficient to trigger 17 spawning migration by the splittail adults, although the BDCP includes monitoring, research, and 18 adaptive management to identify refinements in operations to further increase spawning habitat 19 availability. 20

Restored inundated floodplain habitat in other parts of the Delta would increase habitat 21 availability. Restoration of 10,000 acres of new seasonally inundated floodplain under the 22 BDCP will provide substantial new splittail rearing and spawning habitat in different areas of the 23 Delta in the LLT. Increases in the ELT will be 1,000 acres. Benefits to splittail will occur only 24 with flood events which will be more frequent in wet years, when inundated floodplain habitat is 25 currently most available. The main benefit of this conservation action will be to increase habitat 26 diversity, as discussed below. 27

Enhance channel margin habitat expected to benefit emigrating young of the year (YOY). 28 Currently, channel margin habitat conditions within the Delta are characterized by large areas of 29 riprap stabilized channel margin with little shallow water or low velocity habitat for fry and 30 juvenile rearing. Under the proposed project expansion of access to habitat areas characterized 31 by shallow-water, low-velocities, increased hydraulic residence time, and increased food 32 availability will enhance growth and survival of YOY juvenile splittail during their downstream 33 migrations. Availability of rearing habitat for juveniles during their downstream migration is an 34 important stressor, but less so than the availability of inundated floodplain habitat. Enhancement 35 of channel margin habitat under the proposed project will increase rearing habitat availability 36 and geographic distribution. Channel margin habitat may be used for spawning in dry years, 37 when spawning habitat is limited, but the degree to which splittail spawn in channel margin 38



habitats in the Delta, and conditions required for successful egg/embryo and larval development, 1 are not well known. 2

Restored tidal habitat would provide additional rearing and foraging habitat. Restoration 3 of tidal and subtidal habitats under the proposed project will substantially increase the 4 availability of rearing and foraging habitat for splittail. Availability of rearing habitat for 5 juveniles following completion of their downstream migration is an important stressor, but less 6 so than availability of inundated floodplain habitat. Restoration in the Cache Slough and Suisun 7 Marsh ROAs will be especially beneficial. The Cache Slough area receives most of the YOY 8 splittail emigrating from the Yolo Bypass, resulting in heavy use, whereas Suisun Marsh is the 9 most important rearing habitat destination for juvenile splittail. The benefits of the restored tidal 10 habitats will increase progressively from the NT to the ELT and to the LLT, as areas of restored 11 habitat increase. These benefits could be substantially reduced, however, if non-native 12 vegetation and predatory fish colonize newly restored habitats. Conservation measures to 13 control SAV and non-native predators and the BDCP adaptive management program will be 14 aimed at maintaining high habitat function by addressing these stressors. Tidal habitat may be 15 used for spawning in dry years, when spawning habitat is limited, but the degree to which 16 splittail spawn in tidal habitats in the Delta and the conditions required for successful 17 egg/embryo and larval development are not well understood. 18

Increased Yolo Bypass inundation and channel margin and tidal habitat restoration would 19 result in greater local food production and increased export of production to other areas of 20 the Delta. The increases in Yolo Bypass inundated floodplain habitat and other habitat 21 improvement measures will result in greater food web resources for splittail larvae and juveniles 22 rearing on the floodplain and adults preparing to spawn and for rearing juveniles and foraging 23 adults in channel margin and tidal habitats. More food for splittail will contribute to higher 24 growth rates, survival, and fecundity of splittail. Export of food web resources produced on the 25 floodplain and other restored habitats is expected, which would benefit splittail in other areas, 26 but the degree to which food is exported is uncertain. 27

Habitat restoration over a wide geographic range will have several potential benefits. 28 Restoration of tidal, floodplain, and channel margin habitats under the proposed project will 29 increase the geographic distribution of spawning and rearing habitat for splittail, which will: 1) 30 increase the range of available habitat conditions, thereby improving the likelihood of providing 31 suitable conditions for spawning, eggs/embryo development, larval and juvenile rearing, and 32 adult foraging; and 2) buffer against unforeseen future adverse environmental effects (including 33 catastrophic events). 34

Uncertain effects on exposure to methylmercury. Enhanced frequency and duration of 35 flooding of the Yolo Bypass has the potential to increase exposure of splittail to methylmercury 36 because: 1) the Yolo Bypass experiences high levels of methylmercury loading, particularly from 37 Cache Creek, 2) splittail use of the Yolo Bypass would increase, and 3) the inundation regime on 38 the Bypass will be altered, increasing the rate of mercury methylation. These effects, however, 39



may be mitigated by dilution and advection effects of increased Sacramento River inflows. The 1 thresholds of toxicity of methylmercury concentrations are unknown. The BDCP conservation 2 measure to control methylmercury, implemented with adaptive management, is expected to 3 reduce methylmercury loading. Splittail in Delta habitats are expected to receive increased 4 exposure to methylmercury because habitat restoration activities increase methylmercury 5 production. Splittail are expected to be especially at risk in the Cache Slough ROA because 6 methylmercury concentrations in this area are already high. The BDCP will have a low, but 7 relatively uncertain, negative outcome with regard to methylmercury exposure. 8

Uncertain effects on exposure to pyrethroids. Pyrethroid concentrations in the Delta will 9 decrease under the proposed project during most of the April to July period of juvenile 10 emigration. Residence time also affects exposure to pyrethroids. Residence time, as determined 11 by flow, will increase in some areas of the Delta and decrease in other areas, depending on 12 hydrologic conditions, with no net effect on splittail expected. Habitat restoration under the 13 BDCP will result in reduced pyrethroid loading because agricultural land will be taken out of 14 production. On balance, the BDCP will provide a low, but uncertain, benefit with respect to 15 splittail exposure to pyrethroids. 16

Increased exposure to selenium. The BDCP will result in increased exposure of splittail to 17 toxic levels of selenium. The adult life stage is the most important with regard to selenium 18 because of its relatively long duration and a diet including overbite clams, which contain high 19 concentrations of selenium. Selenium bioaccumulates with age, although eggs and embryos, 20 which receive high levels of selenium in maternal transfer, are the most susceptible to selenium 21 toxicity. The BDCP will result in increased exposure of adults to selenium because it is 22 predicted to cause increased selenium concentrations in the west Delta during the summer and 23 fall. The west Delta is the primary foraging habitat of adult splittail and summer and fall are the 24 principal seasons for grazing by the overbite clam. The effects will be similar in the ELT and 25 LLT relative to EBC, independent of projected climate change. These increases will likely result 26 in increased reproductive failure in splittail, but the magnitude of the effect is uncertain, 27 particularly at the population level. 28

Reduced losses at south Delta SWP/CVP facilities. While it has never been determined that 29 entrainment has a population level effect, reductions in entrainment will increase survival and 30 benefit the species. Dual export facility operations under the proposed project will result in a 31 reduction in juvenile and adult splittail losses at the south Delta export facilities relative to EBC. 32 Juvenile splittail are at risk of losses primarily during May through July, as they migrate to 33 downstream rearing habitats, whereas adult splittail are at risk of loss primarily between 34 December and March, during their upstream spawning migration. The BDCP will result in a 35 substantial reduction in losses of both life stages because exports at the south Delta export 36 facilities, which currently entrain large numbers of splittail, will be reduced, while entrainment 37 of splittail at the new screened north Delta intakes will be negligible. In both the ELT and LLT, 38 the reductions in entrainment of juveniles are predicted to exceed 65 percent at both the CVP and 39 SWP south Delta facilities relative to EBC. For scenarios that take into account projected 40



climate change conditions, the reductions are 75 percent or greater. For adults, the reductions in 1 entrainment at both the CVP and SWP facilities, for all the analysis scenarios, will be between 2 60 and 66 percent relative to EBC. The benefits of these reductions are limited because past 3 studies have found no evidence that entrainment of splittail significantly affects population 4 abundance. The removal of non-project diversions due to changing land use in the Delta as a 5 result of the BDCP will provide a marginal benefit to reducing entrainment risk for larval and 6 juvenile splittail. 7

Effects of BDCP on predation uncertain. Many BDCP conservation actions have the potential 8 to affect predation on splittail, including habitat restoration, changes in lower Sacramento River 9 flow, and north Delta intake structures. Habitat restoration will result in increased numbers of 10 predators and increased numbers of splittail. If predation rates do not change significantly, the 11 net effect will be an increase in the total population of splittail. Diversions of Sacramento River 12 flow at the new north Delta intakes will result in reduced flow rates downstream. Studies on 13 juvenile salmon indicate that flow reductions reduce rates of downstream migration, which 14 increases time of exposure to predators. During May and June, the peak months of juvenile 15 splittail emigration, BDCP operations will reduce average flows by 2 to 3 percent in drier years 16 and 35 to 42 percent in wetter years. When climate change is included, average flows will be 17 negligibly reduced in drier years and reduced by approximately 25 percent in wetter years. The 18 flow reductions will result in little change on predation on juvenile splittail in drier years, but 19 could result in a substantial increase in predation in wetter years. The north Delta intakes will 20 provide new habitat for piscivorous fish such as striped bass, resulting in increased predation on 21 the emigrating juveniles. The increases could be substantial for both the ELT and LLT, 22 exceeding numbers currently entrained at the south Delta facilities. This conclusion is highly 23 uncertain because the actual predation rates by striped bass and other Delta piscivores on splittail 24 are unknown. The BDCP conservation measures to control non-native predators and removal of 25 SAV will result in minor reductions in predation in the Delta. Overall, the BDCP will have 26 moderately negative but uncertain effects with respect to predation on splittail in both the ELT 27 and LLT. 28

Entrainment in Mirant power plants will be greatly reduced. The expected transition to 29 exclusive closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 30 will substantially reduce and avoid entrainment and impingement of juvenile splittail. 31

5.4.1.4.2 Overall Conclusions for Splittail 32 The following overall conclusions were made based on the results of the effects analysis for 33 Sacramento splittail. 34

Contribution to Increased Reproduction. Overall, the BDCP will contribute to increased 35 reproduction of Sacramento splittail. The most important component of the BDCP for splittail is 36 the increase in seasonally inundated floodplain habitat, including expected increases in food web 37 resources. Several studies have concluded that the Sacramento splittail population is largely 38 limited by the availability of floodplain habitat. Splittail year classes are nearly always high in 39



wet years, when large areas of floodplain are inundated, and low in dry years. The BDCP Yolo 1 Bypass floodplain enhancement will substantially increase the acreage of inundated floodplain, 2 particularly in dry years. Restoration of new floodplain under BDCP will provide additional 3 seasonally inundated floodplain habitat, primarily in wet years, and will increase the geographic 4 distribution and diversity of the available habitat for splittail. Restoration of tidal, subtidal, and 5 channel margin habitats under the proposed project will provide additional spawning habitat in 6 all water year types. 7

Need for Adaptive Management. Results of the effects analysis indicate that the BDCP will 8 reduce adverse effects of major stressors and is consistent with, supportive of, and 9 complementary to recovery planning for splittail (USFWS 1996). Uncertainties remain, 10 however, regarding the magnitude of population-level effects on the dynamics and recovery of 11 the population. The BDCP includes adaptive management based on extensive monitoring and 12 research that will be used to address areas of uncertainty and to refine the conservation measures 13 to improve the overall net environmental benefits of the program, in combination with other 14 recovery actions, in contributing to the long-term recovery of splittail. The adaptive ranges for a 15 number of water operations parameters allow for adjustments such that, if initial operations do 16 not support the outcomes expected for splittail, there is the opportunity and flexibility to 17 adaptively change operations and potentially improve biological outcomes. 18

5.4.1.5 Sturgeon 19

5.4.1.5.1 BDCP Effects on Stressors 20 Results of the effects analysis indicate that the BDCP conservation strategy will result in a 21 number of major changes within the Delta that will reduce the impacts of stressors on green and 22 white sturgeon populations and improve habitat conditions for juvenile sturgeon rearing and 23 adult and juvenile sturgeon migration. These major effects analysis findings for stressors on 24 sturgeon are described below. 25

Greater access to rearing habitats potentially used by juvenile sturgeon. BDCP 26 conservation measures will result in substantially increased access to expanded subtidal, tidal 27 wetland and channel margin habitat, geographically located throughout the Delta, which will 28 potentially benefit juvenile sturgeon that utilize the Sacramento River and the San Joaquin River 29 basins, Suisun Marsh and Bay, and the Delta. As noted for salmonids, intertidal habitat will be 30 expanded by approximately 7,900 acres in the NT with an additional 7,300 acres in subtidal 31 habitat. During the ELT, intertidal habitat will be expanded to 13,000 acres and subtidal habitat 32 will be expanded by 9,400 areas. During the LLT intertidal habitat will be expanded by 16,400 33 acres and subtidal habitat will be expanded by 32,300 acres. 34

Habitat benefits for sturgeon. Major expansion in access to tidal habitat and channel margin 35 habitat will result from the proposed project in the northern Delta (Yolo Bypass and Cache 36 Slough complex) as well as channel margin habitat along the mainstem Sacramento River, Sutter 37 and Steamboat sloughs, and western Delta, and tidal habitat expansion within Suisun Marsh that 38



would serve to benefit juvenile sturgeon produced in the Delta. As noted for salmonids, 1 intertidal habitat will be expanded by approximately 3,000 acres in Cache Slough in the NT with 2 an additional 1,200 acres in subtidal habitat. During the ELT, intertidal habitat in Cache Slough 3 will be expanded to 5,900 acres and subtidal habitat will be expanded by 2,300 areas. During the 4 LLT intertidal habitat will be expanded by 6,900 acres from existing conditions and subtidal 5 habitat will be expanded by 7,400 acres. Additional habitat expansion in the western Delta, five 6 miles of channel margin habitat enhancement on the Sacramento River, and substantial increases 7 in habitat in the western Delta and Suisun Marsh will also be made available by the proposed 8 project on the migration pathway for juvenile sturgeon. 9

Expansion of intertidal and subtidal habitat in the south Delta along the migratory pathway for 10 juvenile white sturgeon produced in the San Joaquin River basin will result from the proposed 11 project in the LLT. San Joaquin River white sturgeon will also benefit from subtidal and tidal 12 habitat expansion in the western Delta and Suisun Marsh. 13

Creation of alternative migratory routes and access to more habitat. Juvenile Sacramento 14 River basin sturgeon survival may improve as a result of the potential use of expanded access to 15 seasonal floodplain within the Yolo Bypass, which would provide opportunities for juvenile 16 sturgeon to access alternative migration pathways that would circumvent the north Delta intake 17 structures, the Delta Cross Channel, and Georgiana Slough; 18

BDCP implementation will create conditions of enhanced food production, with potential to 19 offset survival risk from stranding, predation, and water-quality. Expanded access to tidal 20 wetland and improved channel margin habitat will provide shallow water, low-velocity habitat 21 areas with increased food production. Expanded access to suitable habitat will benefit juvenile 22 sturgeon rearing through access to alternative migration pathways, access to improved juvenile 23 rearing habitat, and access to increased food production that collectively are expected to result in 24 increased juvenile growth rates and survival. 25

The magnitude of these benefits on the population abundance of sturgeon from BDCP expanded 26 habitat is uncertain. The potential to improve juvenile sturgeon rearing; and risks associated 27 with predation and exposure to potential toxics and adverse water quality conditions is unknown 28 relative to existing biological conditions. Rigorous monitoring, adaptive management, and 29 continual improvements to habitat restoration design will serve to reduce uncertainty and the risk 30 of adverse effects resulting from habitat expansion. 31

Potential, but unquantified, benefits from habitat modifications along levees. Currently, 32 habitat conditions within the Delta are characterized by large areas of riprap stabilized channel 33 margin with little shallow water or low velocity habitat for juvenile sturgeon rearing. Expanded 34 access under the proposed project to habitat areas characterized by shallow-water, low-velocities, 35 increased hydraulic residence time, and increased food availability, as well as the provision of a 36 wider geographic distribution of diverse and complex habitats within the Delta is consistent with 37 sturgeon conservation, and increases the opportunities for a broader range of life history 38



expression including extended juvenile rearing within the Delta. Expanding opportunities for a 1 wide range of life histories is consistent with sturgeon conservation and recovery principles. 2

Improved survival of juvenile sturgeon from re-operation of the Delta Cross Channel 3 (DCC) gates. Expanded closure of the DCC gates and installation and operation of non-physical 4 barriers at key locations such as the confluence between Georgiana Slough and the Sacramento 5 River and at the head of Old River will improve survival of juvenile sturgeon migrating 6 downstream in the rivers and through the Delta. Extended DCC gate closure may also improve 7 attraction flows and thus improve olfactory cues for upstream migrating adult sturgeon and 8 reduce inter-basin straying. 9

Reduced reverse flow conditions. BDCP dual facility operations will result in substantial 10 improvements in Old and Middle River (OMR) reverse flows within the south and central Delta 11 and a net improvement in downstream flows through the Delta, particularly from the San Joaquin 12 River system. These improvements in Delta hydrodynamics will result in substantial 13 improvements in habitat conditions for juvenile sturgeon rearing and survival in these habitats. 14

Reduced losses of sturgeon in SWP/CVP facilities. While it has never been determined that 15 entrainment has a population level effect, reductions in entrainment will increase survival and 16 benefit the species. Dual export facility operations will result in a reduction in juvenile sturgeon 17 entrainment and salvage losses at the south Delta export facilities by 30-60 percent for white 18 sturgeon and 25-70 percent for green sturgeon relative to existing conditions; 19

Negligible entrainment risk at north Delta intakes. As a result of the state-of-the-art design 20 characteristics (i.e., 0.2 ft/sec approach velocity, screen mesh size, screen cleaning, etc.), and the 21 demersal behavior of post-larval sturgeon, the risk of entrainment of age-0 sturgeon at the north 22 Delta intakes will be negligible, but is currently not quantifiable. 23

Entrainment in non-project diversions will be marginally reduced. The removal of non-24 project diversions due to changing land use in the Delta as a result of the BDCP will provide a 25 marginal benefit to reducing entrainment risk for age-0 sturgeon. 26

Entrainment in Mirant power plants will be reduced. The expected transition to exclusive 27 closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 will 28 substantially reduce and avoid entrainment and impingement of juvenile sturgeon. 29

No adverse upstream impacts on sturgeon. No major adverse effects were detected in the 30 effects analysis on upstream habitat conditions (e.g., reservoir storage, instream flows, and water 31 temperatures during egg incubation) for sturgeon in the Sacramento or San Joaquin rivers. Small 32 positive and negative changes were detected in the Sacramento and Feather rivers, such as 33 reduced summer and fall flows in the Sacramento River relative to existing conditions. None of 34 these changes will have a substantial effect on sturgeon life history (i.e., migration, spawning, 35 and juvenile rearing). No significant changes in upstream habitat (i.e., instream flows and 36



seasonal water temperatures) were detected in the San Joaquin and Stanislaus rivers. BDCP 1 operations will have no effect on habitat in rivers not controlled by the CVP or SWP operations. 2

No increase in egg mortality for Sacramento River or San Joaquin River sturgeon. Results 3 of the SacEFT model for green sturgeon on the Sacramento River indicate an adverse effect on 4 temperature conditions for sturgeon as a result of climate change, but with no apparent effect 5 attributable to the proposed project. Results of the effects analysis detected no BDCP-related 6 adverse effects to upstream habitat conditions (e.g., instream flows, water temperatures during 7 egg incubation) for sturgeon in the Sacramento or San Joaquin rivers. 8

Late summer flow decreases in the Feather River. Within the Feather River, small decreases 9 in July flows under the proposed project, most significant in below normal and dry years in the 10 upper river, may adversely affect green sturgeon egg/embryo; however the adverse affects may 11 be offset by the larger increases in April-June flows under the proposed project, relative to EBC. 12 However, large decreases in late summer flows (Aug-Sept) related to BDCP water operations 13 may adversely affect the downstream migration of green sturgeon larvae. 14

Uncertain Effect of Decrease in Sacramento River flows on adult cue detection. Adult green 15 sturgeon attraction flows from November-July will decrease in the Sacramento River 16 downstream at Rio Vista under proposed project operations. The large decreases in flows at Rio 17 Vista in November were affected not only by north Delta diversions, and the operations of 18 upstream dams, as indicated by the reduced mean monthly flows at Keswick and Verona, but the 19 requirements for cold water pool storage necessary to support upstream salmonid spawning 20 habitat. A good portion of the November-July attraction flow period (December–April) occurs 21 during periods of greatest Sacramento River flows at this portion of the river. Proposed north 22 Delta operations are designed to divert additional waters during the highest flows, to maintain 23 flows during drier periods of the year for threatened and endangered salmonids. However, in the 24 absence of data investigating minimum flow requirements for adult green sturgeon attraction and 25 migratory cues, the certainty at which flow reductions will result in reduced cue detection is low. 26

Uncertain effects related to operation of north Delta intake. Sacramento River flows 27 downstream of the north Delta intakes will be reduced under BDCP operations relative to 28 existing conditions. Flows will be reduced less during the winter than during other seasons. 29 Flows will be reduced most in wet, above normal, and below normal water years; flows are 30 projected to increase under BDCP operations in dry and critical years. The effects of flow 31 reduction within the lower reach of the Sacramento River, on the attraction and olfactory cues for 32 upstream migrating adult sturgeon and survival of downstream migrating juvenile sturgeon are 33 uncertain. 34

Interannual and long-term hydrologic changes occur with or without BDCP operations. 35 The greatest changes in habitat conditions result from natural variation in interannual hydrology 36 (e.g., between wet and dry years) and the effects on hydrology from future climate change. 37 These major effects on habitat were largely independent of differences between existing 38



conditions and BDCP operations. Sturgeon are sensitive to the risk of exposure to elevated water 1 temperatures and decreased flow in the Feather River, potentially decreasing habitat suitability, 2 particularly in drier water years under both existing conditions and proposed BDCP operations. 3

Net benefits of other stressor reduction measures. Collectively, other stressor conservation 4 measures provide additional benefits to sturgeon relative to existing conditions. Benefits of 5 conservation actions such as removing unscreened water diversions and structures that attract 6 predators, although incrementally small, contribute to the cumulative biological benefits of 7 BDCP. Conservation measures with the greatest benefit to sturgeon include the revised 8 operations of Fremont Weir, the installation of 1-3 sturgeon ramps facilitating upstream 9 migration and eliminating the stress of the bottleneck, and the increased game enforcement to 10 significantly reduce the poaching of sturgeon that occurs in the Delta. BDCP will, through the 11 installation of an aeration facility in the Stockton Deep Water Ship Channel (SDWSC), 12 effectively raising dissolved oxygen in much of the channel above levels that cause stress in 13 adult sturgeon. The outcome of this conservation measures will be to reduce the upstream 14 passage impediment of adult sturgeon in the vicinity of the SDWSC and facilitate the migration 15 to suitable upstream spawning habitats in the San Joaquin basin. These other stressors measures, 16 in combination with habitat restoration, will provide the greatest benefit to sturgeon from the 17 proposed project. 18

5.4.1.5.2 BDCP Effects on Green Sturgeon Designated Critical Habitat 19 Critical habitat for green sturgeon was designated in 2009 (74 FR 52300). The effects analysis 20 for green sturgeon addressed how the BDCP would beneficially or adversely affect the primary 21 constituent elements (PCEs) of green sturgeon critical habitat. PCEs in the upstream reaches not 22 affected by BDCP actions and, therefore, not addressed in the effects analysis include substrate 23 type or size and water depth. The green sturgeon PCEs addressed in the effects analysis were: 24

• Freshwater spawning sites (i.e., providing suitable water temperatures, and instream 25 flows for successful spawning in the upstream reaches of the Sacramento River and 26 tributaries); 27

• Freshwater rearing sites (i.e., providing suitable water quality for juvenile rearing, 28 instream flows for downstream migration, sediment quality, tidal habitat and other 29 juvenile rearing areas, and the effect of suitable quantity of food resources for juvenile 30 growth and rearing); 31

• Freshwater migration corridors (i.e., the allowance for safe and timely passage by 32 reducing and avoiding passage barriers and impediments for both juveniles and adults, 33 providing suitable water quality and instream flows to support access and connectivity for 34 migration, both within tidal habitats and through the Delta); 35

• Estuarine areas (i.e., providing safe and timely passage via unobstructed migration and 36 rearing opportunities, suitable water quality with salinity conditions that support juvenile 37 and adult physiological transitions between freshwater and saltwater, sediment quality, 38



and providing food resources to support juvenile, subadult, and adult growth, survival, 1 and facilitate the access to upstream spawning habitats). 2

The effects analysis included a number of analytical approaches, including modeling analyses 3 (i.e. hydrologic and water quality), to predict changes in habitat physical and biological 4 conditions that would potentially affect the quality and availability of suitable habitat influenced 5 by proposed BDCP actions. 6

Effects on Freshwater Spawning Sites. Although minor adverse and beneficial changes in 7 habitat conditions (instream flow, water temperature) were detected for upstream green sturgeon 8 spawning and egg incubation in some locations, these changes will not have a substantive effect 9 on habitat conditions for green sturgeon. The greatest change was noticeable in the reduction of 10 late summer flows in the Feather River. However, as flows are greater in late spring/early 11 summer, it is unknown if these changes will have a substantive effect on habitat conditions in the 12 Feather River. Within the Sacramento and Feather rivers there was little or no cumulative 13 adverse effect of the BDCP on habitat conditions for spawning relative to the EBC. The greatest 14 observed changes in habitat quality or availability are in response to interannual variation in 15 Central Valley hydrologic conditions (e.g., wet years and dry years) and in response to long-term 16 changes in Central Valley climate. Therefore, the proposed project would not affect critical 17 habitat or the success of green sturgeon spawning within the Sacramento or Feather rivers. 18

Effects on Freshwater Rearing Sites. Minor adverse and beneficial changes in habitat 19 conditions (flow and water temperature) were detected for sturgeon rearing. In general, within 20 the Sacramento and Feather rivers, there was no effect of the proposed project on habitat 21 conditions for juvenile rearing relative to the EBC. The greatest observed changes in habitat 22 quality or availability are in response to interannual variation in Central Valley hydrologic 23 conditions (e.g., wet years and dry years) and in response to long-term changes in Central Valley 24 climate. 25

Restoration of additional floodplain, tidal, and channel margin habitat that is geographically 26 distributed throughout the Delta will provide substantial benefits to green sturgeon, with the 27 greatest potential coming through benefits to the foodweb. The predicted magnitude of these 28 benefits to increased juvenile growth and survival, and the contribution of these conservation 29 measures to increased adult sturgeon abundance have not been quantified. Floodplain 30 enhancement actions designed to increase the frequency and duration of seasonally inundated 31 floodplain habitat in Yolo Bypass will be a significant environmental benefit of BDCP. 32 Similarly, BDCP implementation will substantially improve ecological functions and increase 33 the availability of, and access to, intertidal and subtidal habitat that is geographically distributed 34 along the Sacramento River and within the eastern and southern Delta and Suisun Marsh, that 35 will increase rearing habitat and food production for juvenile, subadult, and adult sturgeon, 36 relative to existing conditions. Uncertainty in expanded habitat performance and ecological 37 functions will be addressed through a rigorous BDCP monitoring, research, and adaptive 38 management programs. 39



Overall, the proposed project will not adversely modify habitat conditions for freshwater rearing 1 in upstream habitats within rivers tributary to the Delta. Instead, BDCP conservation actions will 2 improve habitat access, quality, and availability for juvenile green sturgeon in the lower reaches 3 of the Sacramento and Feather rivers and within the Delta and Suisun Marsh. Implementation of 4 BDCP conservation measures will contribute to a substantial increase in suitable habitat for 5 juvenile and subadult rearing. 6

Effects on Freshwater Migration Corridors. The BDCP conservation strategy includes 7 measures specifically designed to improve migratory corridors and reduce the effects of 8 obstructions that impede both juvenile and adult sturgeon passage under existing conditions. 9 Proposed actions include improving passage at the Fremont Weir through the installation of 10 sturgeon ramps, notching the weir, increasing game enforcement to reduce the poaching of adult 11 sturgeon, increasing closure of the Delta Cross Channel gates to improve migration and upstream 12 cue detection. Operations under BDCP will also improve hydrologic conditions as reflected by 13 an increase in positive flows in Old and Middle rivers, as well as maintenance of instream flows 14 within the tributaries to the Delta. These conditions are intended to improve the survival of 15 juvenile sturgeon migrating downstream through the Delta, in part by reducing their vulnerability 16 to entrainment losses at the existing south Delta water export facilities. Restoration of additional 17 floodplain and tidal habitat would be beneficial for sturgeon. There is a high degree of 18 uncertainty, however, in the quantification of the magnitude of net benefits to sturgeon 19 populations. Reductions in instream flow in the lower reaches of the Sacramento River have the 20 potential to reduce olfactory cues and attraction flows for upstream migrating adult sturgeon, and 21 river flows for downstream migrating juveniles. Upstream of the north Delta intakes, river flows 22 are similar between the proposed project and existing conditions. In the vicinity of Rio Vista, 23 flows would be reduced during the period for upstream cue detection. The effect of this 24 reduction on population dynamics is currently unknown. In the downstream estuarine region of 25 the Delta, tidal flows are dominant. No information is available to quantitatively assess the 26 potential effects of local flow reductions on migration and survival of green sturgeon. 27

Overall, the BDCP will not adversely modify habitat conditions for green sturgeon migration 28 corridors within the tributaries of the Delta and would improve passage conditions for green 29 sturgeon migrating through the Delta. BDCP conservation actions will reduce obstruction to 30 juvenile and adult sturgeon passage within the lower reaches of the Sacramento River and 31 throughout the Delta and Suisun Marsh. Implementation of BDCP conservation measures is 32 expected to contribute to an increase in habitat conditions for juvenile and adult sturgeon 33 migration. 34

Effects on Estuarine Areas. The BDCP conservation strategy will contribute to a substantial 35 increase in access to suitable juvenile and subadult green sturgeon rearing habitat within the 36 estuarine regions of the Delta through channel margin habitat enhancements in the western Delta, 37 as well as substantial increases in aquatic habitat within Suisun Marsh adjacent to Suisun Bay 38 (approximately 24,570 acres in the LLT). The increased access of intertidal and shallow subtidal 39 rearing habitat within the estuarine region of the Delta will contribute to an increase in ecological 40



functions of aquatic habitat including increased habitat diversity and complexity, foraging habitat 1 and food resources for juvenile green sturgeon. Restoration of additional tidal habitat will be 2 beneficial to green sturgeon. Although positive trends towards recovery are anticipated, there is 3 a high degree of uncertainty in the magnitude of net population level benefits to green sturgeon. 4

Water operations under the proposed project will improve hydrologic conditions as reflected by 5 an increase in positive flows in Old and Middle rivers and maintenance of instream flows within 6 the rivers tributary to the Delta. These conditions will improve the survival of juvenile sturgeon 7 migrating downstream through the Delta and improve estuarine rearing habitat conditions. 8 These improvements will benefit juvenile green sturgeon by providing a potential for increased 9 growth conditions, which should contribute to increased survival. Improvements in central Delta 10 habitat and hydrodynamics will provide the greatest benefits for green sturgeon rearing in 11 estuarine habitats. 12

Overall, the BDCP will not adversely modify habitat essential for green sturgeon within the 13 estuarine region of the Delta. The BDCP will contribute to an increase in habitat for juvenile and 14 subadult green sturgeon migration within the estuarine region of the Delta. 15

5.4.1.5.3 Overall Conclusions for Sturgeon 16 The following overall conclusions were made based on the results of the effects analysis for 17 green and white sturgeon. 18

Contribution to Recovery. BDCP conservation measures are consistent with and 19 complementary to sturgeon recovery within the Central Valley. In addition to habitat benefits 20 provided by BDCP conservation measures, additional measures to reduce poaching and facilitate 21 upstream migration will increase the protection and survival of reproducing members of the 22 populations. There are no actions proposed as part of BDCP that are inconsistent or incompatible 23 with long-term sturgeon recovery; 24

Net Beneficial Effects on Designated Critical Habitat. BDCP conservation actions would 25 contribute substantially to improved habitat availability and diversity that would benefit green 26 sturgeon by reducing stressors that currently affect growth, survival, migration, and population 27 abundance. These improvements in critical habitat conditions for green sturgeon would 28 contribute to increased juvenile growth and survival, greater life history and habitat diversity, 29 and are expected to result in increased green sturgeon abundance. Effects of BDCP operations 30 on critical habitat upstream of the Delta has been evaluated and results show relatively small 31 adverse and beneficial effects on habitat conditions for spawning and juvenile rearing on the 32 mainstem Sacramento River and Feather River. The magnitude of beneficial effects associated 33 with changes in water operations, expanded aquatic habitat, improved hydrologic conditions in 34 the Delta, and reduction in other stressors such as poaching and migration barriers have not been 35 quantified. Uncertainties regarding the ecological functions and net biological response of green 36 sturgeon to expanded diverse habitats geographically distributed in various regions of the Delta, 37 and changes in water operations and hydrologic conditions within the rivers and Delta, will be 38



addressed through the monitoring, research, and adaptive management programs. Therefore, the 1 construction and operation of the proposed project, including adaptive management actions, 2 would not be expected to adversely modify green sturgeon critical habitat. 3

Need for Adaptive Management. As a comprehensive package of conservation measures, 4 BDCP will contribute to the survival and recovery of white and green sturgeon through 5 cumulative reduction in stressors and improvements in habitat, that together contribute to 6 increased population abundance. The magnitude of the effects of BDCP actions on green 7 sturgeon recovery, however, has not been quantified. There remain areas of uncertainty 8 regarding the effectiveness of various individual conservation actions that will be addressed as 9 part of BDCP implementation through the BDCP monitoring, research, and adaptive 10 management programs. 11

5.4.1.6 Lamprey 12

5.4.1.6.1 BDCP Effects on Stressors 13 Based on results of the effects analysis, implementation of the BDCP conservation strategy will 14 result in a number of changes that will reduce the impacts of stressors on Pacific and river 15 lamprey. Some adverse effects were also noted. These effects analysis findings include: 16

No major effects on downstream migration flows in most rivers. There are no measurable 17 predicted effects of BDCP on downstream macropthalmia migration of changes in flows in the 18 Sacramento, San Joaquin, or Stanislaus rivers. Flow effects on downstream macropthalmia 19 migration during December through May in the Feather River will improve by 5 to 25 percent as 20 a result of the proposed project. There is a 3-15 percent predicted reduction in flows in the 21 Sacramento River in the Delta. Climate change will generally increase flows during January 22 through March and decreases flows during May. There is moderate certainty regarding these 23 conclusions because they are based entirely upon model output. 24

Within the Delta, upstream migration conditions will greatly improve in the San Joaquin 25 River but decline slightly in the Sacramento River. As a result of changes in diversion points 26 and dual operations under the proposed project, there will be large benefits to San Joaquin River 27 attraction flows for both Pacific lamprey (mean increases during December through May of 36-28 146 percent) and river lamprey (mean increases during September through November of 374-733 29 percent) under the proposed project. In addition, passage impediments such as the Stockton 30 Deep Water Ship Channel low dissolved oxygen barrier will be reduced significantly as a result 31 of the proposed project. There will be small reductions in attraction flows for Pacific lamprey 32 adults in the Sacramento River (predicted 4-12 percent reduction in mean in-Delta attraction 33 flows) and moderate reductions for river lamprey in the Sacramento River (predicted 11-17 34 percent in mean in-Delta attraction flows). Climate change is predicted to have variable effects 35 on Sacramento River contributions and marginal benefits in the San Joaquin River to lamprey 36 attraction flows. There is low certainty in these conclusions because of limited understanding of 37 the use of upstream migration cues by lamprey. 38



Upstream of the Delta, there are small benefits or no changes in predicted adult Pacific 1 lamprey attraction flows and highly variable, but predominantly adverse predicted effects 2 on river lamprey attraction flows. There will be no effects of the proposed project on Pacific 3 lamprey adult attraction flows during December through May in the Sacramento, San Joaquin, or 4 Stanislaus rivers. There will be small benefits to Pacific lamprey in the Feather and American 5 rivers due to changes in upstream reservoir operations. For river lamprey, there will be highly 6 variable, but predominantly reduced, adult attraction flows during September through November 7 upstream of the Delta in the Sacramento, Feather, Trinity, and American rivers. There will be no 8 effects in the Stanislaus or San Joaquin rivers to river lamprey. There are minimal and 9 inconsistent effects of climate change on these upstream flows during January through June 10 (Pacific) and September through November (river). There is low certainty in these conclusions 11 due to limited understanding of the use of upstream migration cues by Pacific and river lamprey. 12

No major effects on upstream water temperatures. Upstream water temperatures during egg, 13 embryo, and ammocoete occurrence for both Pacific and river lamprey will not change in a 14 measurable or consistent way as a result of the proposed project. Climate change is predicted to 15 moderately increase water temperature and this effect far outweighs effects of the proposed 16 project. There is moderate certainty regarding these conclusions because multiple models were 17 used to derive temperature outputs. 18

No major effects on redd dewatering incidence in most rivers. Predicted changes in redd 19 dewatering incidence for both Pacific and river lamprey will be small and inconsistent among all 20 evaluated locations except for the Feather River. The incidence of redd dewatering in the 21 Feather River will increase moderately in both the ELT and LLT. Climate change has small and 22 variable effects on redd dewatering. However, due to the lack of instream models available for 23 lamprey redds, there is low certainty that the metric used in this analysis (50 percent reduction 24 month-over-month instream flows) represents actual redd dewatering, although they are likely 25 correlated. 26

Entrainment in SWP and CVP intakes will be moderately reduced. While it has never been 27 determined that entrainment has a population level effect, small reductions in entrainment will 28 increase survival and benefit the species. Entrainment and impingement of both Pacific and river 29 lamprey at the north Delta diversions will be minimal because of the size and swimming ability 30 of macropthalmia at the time of passage past the intakes compared to the slot size of screens and 31 approach velocity. In the south Delta, entrainment will decline by approximately 40-50 percent 32 due to reduced diversions and the change in seasonal timing of diversions in the south Delta. 33 Climate change effects will be small relative to the reductions by the BDCP and inconsistent 34 among months and between SWP and CVP facilities. The certainty regarding these results is 35 limited due to high temporal variability in salvage numbers. 36

Entrainment in non-project diversions will be marginally reduced. The removal of non-37 project diversions due to changing land use in the Delta as a result of the implementation of 38 BDCP habitat restoration will provide a marginal benefit to both Pacific and river lamprey 39



macropthalmia. Climate change is not expected to affect these results. There is relatively low 1 certainty in these results due to the lack of rigorous sampling of agricultural diversions to date. 2

Entrainment in Mirant power plants will be greatly reduced. The transition to exclusive 3 closed cycle water use at Mirant’s Contra Costa and Pittsburg power plants by 2017 will greatly 4 reduce entrainment of both Pacific and river lamprey macropthalmia. Climate change is not 5 expected to affect these results. Because the effect of entrainment at power plants under existing 6 biological conditions is not well understood, the magnitude of this benefit is uncertain. 7

Upstream predation will not change; Delta predation will increase. Changes to potential 8 upstream predator abundance and consumption rates of both Pacific and river lamprey eggs, 9 embryos, and ammocoetes as measured by water temperature will not change due to the 10 proposed project because temperatures would increase only 1-2 °F. However, there are slightly 11 greater predicted temperature increases (1-4 °F) due to climate change. There is low certainty of 12 these conclusions due to lack of understanding of predation pressure on Pacific and river lamprey 13 and lack of direct analysis on predator abundance and consumption rates. 14

Predation rates of both Pacific and river lamprey macropthalmia at the north Delta diversion 15 intake will increase from background predation rates. Some of this increase will be offset by 16 predator reduction actions under the proposed project at the intake facilities and other predator 17 hotspots in the Delta, although these actions are predicted to provide short-term, small scale 18 benefits. Climate change may increase predation rates because predators will need to consume 19 more to keep up with their increased temperature-dependent metabolism. There is low certainty 20 regarding these results due to a lack of understanding of predation rates of lamprey fish predators 21 that would be attracted to the north Delta intakes. 22

5.4.1.6.2 Overall Conclusions for Lamprey 23 The following overall conclusions were made based on the results of the effects analysis for 24 Pacific and river lamprey. 25

Contribution to Reduction in Stressors. Overall, the BDCP will contribute to the net reduction 26 in adverse stressors on both Pacific and river lamprey. Positive upstream effects on flow and 27 water temperatures at some locations and during some months will outweigh adverse effects, 28 even though most of the upstream effects are small. The reduction in attraction flows in the 29 Sacramento River below the new intakes will be partially offset by improved Yolo Bypass flows 30 and large improvements in the San Joaquin River. Predation effects on lamprey at the north 31 Delta intakes will be greater than the reduction in entrainment effects in the south Delta. The 32 collective benefits of additional BDCP actions, including predator control, non-project 33 entrainment reductions, and power plant entrainment reductions will add to the benefits to 34 lamprey populations. 35

Need for Adaptive Management. The results of the effects analysis indicate that the proposed 36 water project operations would avoid and minimize adverse effects on lamprey and, in 37



combination with other conservation measures, contribute to recovery of the two lamprey 1 species. There are many uncertainties regarding the magnitude of population-level effects of the 2 BDCP on the dynamics and recovery of the species. The BDCP includes adaptive management 3 based on extensive monitoring and research that will be used to address areas of uncertainty and 4 to refine the conservation measures to improve the overall net environmental benefits of the 5 program, in combination with other recovery actions, in contributing to the long-term recovery 6 of lamprey. The adaptive ranges for a number of water operations parameters allow for 7 adjustments such that, if initial operations do not support the outcomes expected for lamprey, 8 there is the opportunity and flexibility to adaptively change operations and potentially improve 9 biological outcomes. 10

[Note to Reviewers: the following are the draft natural communities and covered wildlife and 11 plant species sections of Chapter 5, Effects Analysis, for the November 18, 2010 BDCP 12 document. These sections consist of revised “summary of effects” sections from the August 19, 13 2010 draft for the natural communities and species for only the late long-term outcomes with full 14 BDCP implementation. The text has been modified to indicate whether or not restoration/ 15 protection of natural communities and habitats will keep pace with the expected rate of impacts. 16 The results include the “population-level” effects section for each of the covered species and the 17 assessment of effects on critical habitat for applicable species. The “estimated level of take” 18 sections from that document are not included. Tables presenting the extent of impacts on and the 19 level conservation provided for each of the natural communities and covered wildlife and plant 20 species habitats at the late long-term evaluation point are provided at the end of this draft.] 21

5.4.2 Natural Communities 22

The following summarizes the overall effects of implementing the BDCP actions on each of the 23 natural communities. The extent of each natural community that would be permanently and 24 temporarily removed and periodically affected by BDCP at the late long-term evaluation point is 25 presented in Table 5-1. The table also indicates the total extent of each natural community that 26 will be present in the Plan Area following full implementation of the BDCP. The extent of the 27 contribution to conservation of each natural community following full BDCP implementation 28 through implementation is presented in Table 5-2. The complete effects analysis will describe 29 the combined effects of implementing all BDCP actions for each of the natural communities at 30 the near-term, early long-term, and late long-term evaluation periods. 31

The complete effects analysis will present the permanent, temporary, and periodic effects on 32 each natural community for each of the evaluation periods for the entire Plan Area and each of 33 the 11 Plan Area Conservation Zones (see Figure 3-1) and will describe the combined effects of 34 implementing all BDCP actions for each of the natural communities at the near-term, early long-35 term, and late long-term evaluation periods. The mechanisms associated with each of the BDCP 36 actions that can result in a permanent or temporary direct or indirect effect, or periodic effect on 37 each of the natural communities will also be described and evaluated in the full effects analysis. 38



5.4.2.1 Tidal Perennial Aquatic Natural Community 1

The implementation of all BDCP actions would result in overall benefits for the tidal perennial 2 aquatic community, including the restoration and ongoing management of subtidal aquatic 3 habitats and a return to more-natural channel water salinity in habitats restored in Suisun Marsh. 4 Based on RMA modeling of hypothetical tidal habitat restorations (see Appendix N.3), 5 approximately 25,000 to 32,000 acres of tidal perennial aquatic natural community would be 6 restored, resulting in a 29 to 37 percent increase in subtidal aquatic habitat in the Plan Area (see 7 Table 5-1). The export of nutrients and food restored tidal marsh plains, floodplain, and channel 8 margin habitats would improve the habitat functions of the tidal perennial aquatic community for 9 covered fish species and other aquatic species. Improvements in the habitat function of the tidal 10 perennial aquatic community for covered fish species and other aquatic species would result 11 from BDCP actions specifically designed for or incidentally resulting in the reduction of 12 stressors such as nonnative predators, nonnative invasive plant species, and agricultural 13 pesticides and herbicides. BDCP actions are estimated to remove 46 acres of the tidal perennial 14 aquatic community, amounting to less than 2 percent of the extent of BDCP restored tidal 15 perennial aquatic community (Table 5-2). There are no temporal losses of the community 16 because the extent that would be removed by the covered activities at each evaluation point is 17 exceeded by the extent of tidal perennial aquatic community that would be restored. 18

5.4.2.2 Tidal Mudflat 19

The implementation of the BDCP would result in overall benefits for the tidal mudflat 20 community through the restoration of at least 20 linear miles of tidal mudflat edge as a 21 component of the 65,000 acres of BDCP restored tidal and channel margin habitats. This 22 increase in the extent of tidal mudflat is expected to provide foraging habitat for shorebirds, 23 wading birds, and other native wildlife species as well as substrates suitable for the establishment 24 of covered and other tidal mudflat plant species. Implementation of the covered activities is 25 expected to affect an indeterminable extent of tidal mudflat through construction of new intake 26 facilities and restoration of tidal, floodplain, and channel margin habitats. Restoration of tidal, 27 floodplain, and channel margin habitats, however, are expected to result in an overall increase in 28 the extent of tidal mudflat. Changes in water operations may also affect the long-term 29 distribution of tidal mudflat if those changes alter the current patterns of erosion and deposition 30 in tidal channels. No temporal losses of tidal mudflats are expected because the extent that 31 would be removed by the covered activities at each evaluation point is expected to be exceeded 32 by the extent of tidal mudflat that would be restored. 33

5.4.2.3 Tidal Brackish Emergent Wetland 34

Implementation of the BDCP would result in overall benefits for the tidal brackish emergent 35 wetland community, including the restoration and ongoing management of tidal brackish 36 emergent wetlands and a return to more-natural channel water salinity. Based on RMA 37 modeling of hypothetical tidal habitat restorations (see Appendix N.3), between 3,600 and 4,800 38 acres of tidal brackish emergent wetland community would be restored in Suisun Marsh 39



(Conservation Zone 11), resulting in a 37 to 51 percent increase in the tidal brackish emergent 1 wetland community in the Plan Area (see Table 5-1). There are no temporal losses of the 2 community because the extent of tidal brackish emergent wetland that would be removed by the 3 covered activities at each evaluation point is exceeded by the extent of tidal brackish emergent 4 wetland that would be restored. Restoration and subsequent management of this community to 5 maintain its ecological functions is expected to benefit aquatic food web processes in support of 6 the covered and other native fish species and covered and other native wildlife and plant species 7 dependent on Suisun Marsh tidal habitats. 8

5.4.2.4 Tidal Freshwater Emergent Wetland Natural Community 9

The implementation of the BDCP would result in overall benefits for the tidal freshwater 10 emergent wetland community through restoration and ongoing management of the community. 11 Based on RMA modeling of hypothetical marsh restorations, between 13,200 to 21,600 acres of 12 tidal freshwater emergent wetland community would be restored in the Cache Slough Complex, 13 the South Delta, the Cosumnes/Mokelumne, and the West Delta ROAs (Conservation Zones 1, 2, 14 and 4-7), more than doubling the total extent of tidal freshwater emergent wetland community in 15 the Plan Area (Table 5-1). The restored areas of tidal freshwater emergent wetland community 16 are expected to support higher habitat functions for associated-covered and other native wildlife 17 species because they are expected to be much larger than the existing tidal freshwater emergent 18 wetlands that primarily occur in small and isolated patches. There are no temporal losses of the 19 community because the extent of tidal brackish emergent wetland that would be removed by the 20 covered activities at each evaluation point is exceeded by the extent of tidal brackish emergent 21 wetland that would be restored. Restoration and subsequent management of this community to 22 maintain its ecological functions is expected to benefit aquatic food web processes in support of 23 the covered and other native fish species and covered and other native wildlife and plant species 24 associated with tidal habitats of the Delta. 25

5.4.2.5 Valley/Foothill Riparian Natural Community 26

Implementation of the BDCP would result in overall benefits for the valley/foothill riparian natural 27 community through restoration and ongoing management of 5,000 acres of riparian communities. 28 BDCP actions are expected to permanently and temporarily remove and periodically inundate 29 1,114 acres, 165 acres, and 589 acres of riparian habitats, respectively (Table 5-1). Following 30 implementation of riparian restoration actions, there would be a 22 percent increase in the total 31 extent of riparian habitats in the Plan Area and an 80 percent increase in the amount of protected 32 riparian habitat in the Plan Area (Tables 5-1 and 5-2). Restored riparian natural community is 33 expected to support higher habitat functions for associated covered and other native wildlife 34 species because restoration would occur in large patches within floodplains and along channel 35 margins compared with the small, narrow, isolated patches of existing riparian habitat in the Plan 36 Area. Restored sites would also provide more structural and species diversity than most existing 37 patches with an increase in ecological function. There is a temporal loss of riparian habitat because 38 most of the affected riparian vegetation is removed in the near-term implementation period, while 39



large quantities of riparian habitat will not be restored until the early and late long-term 1 implementation periods (Figure 5-3). 2

Each mapped polygon of riparian vegetation that would be removed by BDCP actions were 3 categorized as supporting low, moderate, or high habitat functions for the riparian-associated and 4 other native wildlife based on the following criteria: 5

• Type of vegetation (woodland, scrub, or herbaceous), 6

• Extent and structural qualities of riparian vegetation (dense multistoried vegetation versus 7 a few trees with no understory) within the polygon, 8

• Hydrology and connectivity (along an active natural stream, man-made canal, irrigation 9 ditch, or isolated patch with no riparian function), and 10

• Polygon size. 11

Based on this assessment, Figure 5-3 illustrates the extent of affected riparian vegetation that 12 support low, moderate, and high wildlife habitat values, and Figure 5-4 depicts the size 13 distribution of affected riparian vegetation polygons as an indicator of habitat patch size. 14

Effects of this temporal loss of riparian communities on associated covered and other native 15 wildlife species is expected to be minimal because most of the affected community is comprised 16 of small patches of riparian scrub and herbaceous vegetation that are fragmented and distributed 17 across the agricultural landscape of the Plan Area. Consequently, much of the affected 18 valley/foothill riparian natural community supports relatively low-functioning habitat for 19 associated covered species and other native species and is not expected to result in a measurable 20 change in the abundance or distribution of these species in the Plan Area. Restoration and 21 subsequent management of this community are expected to benefit covered species habitat and 22 food web processes and result in an increase in ecological function as large stands of new valley 23 foothill riparian community develop within natural landscape and hydrological positions. Figure 24 5-3 illustrates the expected development of restored riparian habitat functions over time for the 25 riparian-associated covered wildlife species. 26

5.4.2.6 Grassland Natural Community 27

The implementation of the BDCP would result in overall benefits for the grassland community 28 through protection and enhancement of existing and restoration of 10,000 acres of grassland 29 habitats. These conservation actions would increase the amount of grassland with protected status 30 in the Plan Area from a current 14,984 acres, or 24 percent, to approximately 23, 955 acres, a 60 31 percent increase in the extent of protected habitat area (Table 5-2). BDCP actions are expected to 32 permanently, temporarily, and periodically remove 2,831 acres, 437 acres, and 2,111 acres of 33 grassland, respectively (Table 5-1). Sufficient grassland habitat, however, will be protected, 34 enhanced, and restored at each of the evaluation points to address any temporal loss of habitat 35 functions and to contribute to the conservation of grassland-associated covered and other native 36 species. 37



Figure 5-3. Cumulative Riparian Habit Restoration versus Cumulative Permanent Removal



Figure 5-4. Size Distribution of Affected Riparian Forest and Scrub Polygons



Figure 5-5. Maturation and Succession of Restored Riparian Forest and Scrub and Use by Covered Wildlife Species



The 1,854 acres of grassland removed as a result of tidal and associated riparian habitat 1 restoration are subsided, historically supporting tidal habitats rather than grassland (Table 5-1). 2 Furthermore, most of the grassland to be removed consists of naturalized communities of exotic 3 species on lands that were drained for agriculture and on levees; these communities typically 4 support low ecological functions for covered species and other native species. With restoration 5 of 2,000 acres of grassland, there would be a net loss of 823 acres of grassland from the Plan 6 Area (Table 5-1). In contrast to most of the removed grasslands, the grasslands to be protected, 7 enhanced, and restored would be in landscape positions at which grasslands occurred 8 historically. Existing unprotected grassland would be protected in large patch sizes connected to 9 existing large areas of grassland that would serve as gene dispersal and migration corridors as 10 well as transitional habitat areas to maximize the ecological functions of the grasslands for 11 covered and other native wildlife and plant species. The overall habitat quality of protected, 12 enhanced, and restored grassland is expected to be greater than the grasslands adversely affected 13 by the BDCP. 14

5.4.2.7 Alkali Seasonal Wetland Complex 15

The implementation of the BDCP would result in overall benefits for the alkali seasonal wetland 16 complex community through protection and enhancement of 400 acres of existing alkali seasonal 17 wetland complex. Priority for protection under the BDCP is given to alkali seasonal wetlands 18 that support occurrences of covered plant species, thus contributing to their conservation (e.g., 19 heartscale, brittlescale, and Carquinez goldenbush). These conservation actions would increase 20 the extent of protected alkali seasonal wetland complex in the Plan Area to 87 percent, 21 representing a 12 percent increase in the extent protected. BDCP actions could permanently 22 remove up to 136 acres and increase the extent of alkali seasonal wetland complex periodically 23 inundated in the Yolo Bypass by 825 acres (Table 5-1). Sufficient alkali seasonal wetland 24 complex, however, will be protected and enhanced at each of the evaluation points to address 25 any temporal loss of habitat functions and to contribute to the conservation of alkali seasonal 26 wetland complex -associated covered and other native species. 27

Existing unprotected alkali seasonal wetland complex would be protected in conjunction with 28 protected and restored grassland and vernal pool complex to establish large mosaics of these 29 interdependent communities that are connected to existing large areas of grassland. These large 30 patches of protected communities would serve as gene dispersal and migration corridors as well 31 as transitional habitat areas to maximize the ecological functions of protected the alkali seasonal 32 wetland complex for covered and other native species. Consequently, the overall habitat quality 33 of the protected and enhanced alkali seasonal wetland complex is expected to be greater than the 34 affected alkali seasonal wetland complex. 35

5.4.2.8 Vernal Pool Complex 36

The implementation of the BDCP would result in overall benefits for the grassland community 37 through protection and enhancement of existing and restoration of 500 acres of vernal pool 38 complex. Priority for protection under the BDCP is given to vernal pool complex that support 39



occurrences of covered plant species, thus contributing to their conservation (e.g., San Joaquin 1 spearscale, dwarf downingia, and delta button celery). These conservation actions would 2 increase the extent of protected vernal pool complex to 69 percent, representing an 11 percent 3 increase in the extent of protected vernal pool complex in the Plan Area (Table 5-2). BDCP 4 actions could permanently remove up to 88 acres of vernal pool complex as a result of restoring 5 tidal habitats (Table 5-1). Sufficient vernal pool complex, however, will be protected and 6 enhanced at each of the evaluation points to address any temporal loss of habitat functions and to 7 contribute to the conservation of vernal pool complex-associated covered and other native 8 species. 9

Existing unprotected vernal pool complex would be protected and restored in conjunction with 10 protected and restored grassland and the alkali seasonal wetland complex to establish large 11 mosaics of these interdependent communities that are connected to existing large areas of 12 grassland. These large patches of protected communities would serve as gene dispersal and 13 migration corridors as well as transitional habitat areas to maximize the ecological functions of 14 protected and restored vernal pool complex for covered and other native species. Consequently, 15 the overall habitat quality of the protected, enhanced, and restored vernal pool complex is 16 expected to be greater than the affected vernal pool complex. 17

5.4.2.9 Other Natural Seasonal Wetlands 18

Implementation of BDCP actions would permanently remove 1 acre of other natural seasonal 19 wetlands, representing less than 1 percent of the existing extent of this community in the Plan 20 Area, and would increase inundation frequency of 2 acres on restored floodplains (see 21 Table 5-1). Protection, enhancement, and management of other natural seasonal wetlands that 22 are present on agricultural lands acquired in fee-title would prevent removal or degradation of 23 other natural seasonal wetlands that function as habitat for covered species resulting from future 24 changes in land use. Enhancement and management of protected wetlands would increase their 25 function as habitat for associated covered plant and other native species. 26

5.4.2.10 Nontidal Freshwater Perennial Emergent Wetland 27

Implementation of the BDCP would result in an overall benefit for the nontidal freshwater 28 permanent emergent wetland community through restoration of 400 acres of high functioning 29 nontidal freshwater marsh, of which the nontidal freshwater permanent emergent wetland 30 community will be a component. If at least 200 acres comprises nontidal freshwater permanent 31 emergent wetland, there would be a net increase of 108 acres (approximately 10 percent) of 32 nontidal freshwater permanent emergent wetland in the Plan Area (Table 5-1) and a 37 percent 33 increase in the amount of protected nontidal freshwater permanent emergent wetland in the Plan 34 Area (Table 5-2). The 400 acres of nontidal freshwater marsh will be restored in the near-term 35 implementation period, thus minimizing any temporal loss of habitat functions associated with 36 implementation of BDCP actions on the community. Restored nontidal freshwater marsh would 37 be designed primarily to benefit giant garter snake and other wetland species in Conservation 38 Zones 2 and 4. Restored nontidal freshwater marsh is expected to support higher habitat 39



functions for associated covered and other native species because restoration would occur in 1 relatively large patches compared with the small, isolated patches that currently exist in the Plan 2 Area. 3

Restoration of 400 acres of nontidal marsh is expected to increase the extent of high value 4 emergent marsh habitat for giant garter snake, western pond turtle, and other native wildlife 5 species (e.g., wintering and resident waterfowl). In addition to restoration and enhancement of 6 habitats that support native wildlife species associated with the nontidal freshwater permanent 7 emergent wetland community, existing emergent marsh habitats present on BDCP-protected 8 lands would be managed to maintain and, where appropriate, increase their habitat functions in 9 support of covered and other native wildlife species (e.g., modifying agricultural conveyance 10 maintenance practices to minimize effects on associated wildlife). 11

5.4.2.11 Nontidal Perennial Aquatic Natural Community 12

Implementation of the BDCP would result in an overall benefit for the nontidal perennial aquatic 13 natural community through restoration of 400 acres of high functioning nontidal freshwater 14 marsh, of which the nontidal perennial aquatic natural community will be a component. If at 15 least 200 acres of the restored marsh is comprised of nontidal perennial aquatic habitat, there 16 would be a loss of 45 acres (0.9 percent) of nontidal perennial aquatic natural community in the 17 Plan Area (Table 5-1) and a 12 percent increase in the amount of protected nontidal perennial 18 aquatic community in the Plan Area (Table 5-2). The majority of removed nontidal perennial 19 aquatic community is associated with agricultural ditches and drains and support limited 20 ecological function. Restored nontidal freshwater marsh would be designed primarily to benefit 21 giant garter snake and other wetland species in Conservation Zones 2 and 4. While non-tidal 22 freshwater marsh would be protected on BDCP lands, directed restoration and management of 23 400 acres would occur primarily to benefit giant garter snake and other wetland species in 24 Conservation Zones 2 and 4. Restored nontidal freshwater marsh is expected to support higher 25 habitat functions for associated covered and other native species because restoration would occur 26 in relatively large patches compared with the small, isolated patches that currently exist in the 27 Plan Area. Restoration of 400 acres of nontidal marsh is expected to increase the extent of high 28 value open water habitat for giant garter snake, western pond turtle, and other native wildlife 29 species (e.g., wintering and resident waterfowl). In addition to restoration and enhancement of 30 habitats that support native wildlife species associated with the nontidal perennial aquatic 31 community, existing open water habitats present on BDCP-protected lands would be managed to 32 maintain and, where appropriate, increase their habitat functions in support of covered and other 33 native wildlife species (e.g., modifying agricultural conveyance maintenance practices to 34 minimize effects on associated wildlife). 35

5.4.2.12 Inland Dune Scrub Natural Community 36

Implementation of the BDCP would result in overall beneficial effects on the inland dune scrub 37 community. No BDCP actions would affect inland dune scrub natural community. The BDCP 38 would result in an overall benefit to the ecological function of the inland dune scrub community 39



in the Plan Area though financially supporting the USFWS’ existing restoration, long-term 1 management, and enhancement of the community. 2

5.4.2.13 Managed Wetlands 3

The implementation of BDCP actions are expected to remove 12,196 acres of managed wetlands, 4 primarily from Suisun Marsh as a result of restoration of tidal habitats (see Appendix N.3, RMA 5 Description of Hypothetical Restoration Design and Effects). The habitat functions provided by 6 these managed wetlands for associated covered wildlife species are also supported by natural 7 communities (e.g., tidal and grassland habitats) and agricultural habitats that will be protected, 8 enhanced, and restored under the BDCP. Based on the assessment of effects on these covered 9 wildlife species (see Section 5.5.3, Covered Wildlife and Plant Species), protection, 10 enhancement, and restoration of these replacement habitats are expected to result overall benefits 11 for covered wildlife species that use managed wetlands. Managed wetlands are typically 12 managed to provide habitat for wintering waterfowl and migrant shorebirds. As described for 13 covered wildlife species, protection, enhancement, and restoration of natural communities and 14 agricultural habitats also provide waterfowl and shorebird habitats. Based on an evaluation of 15 the effects of BDCP actions on the waterfowl and shorebird habitat functions provided by 16 affected managed wetlands and other natural communities, implementation of BDCP habitat 17 conservation measures are expected to replace or provide greater habitat functions for these 18 species than the affected waterfowl and shorebird habitats (see Appendix N.6, Waterfowl and 19 Shorebirds Effects Analysis). Consequently, although BDCP actions will result in a reduction in 20 the extent of managed wetlands within the Plan Area, the habitat functions for covered and other 21 native wildlife species that use managed wetlands are expected to be maintained or increased 22 beyond current conditions. 23

5.4.2.14 Agricultural Land 24

Implementation of the BDCP would result in an overall benefit to the ecological function of 25 agricultural lands as habitat for associated covered species through protection and enhancement 26 of 16,620 to 32,640 acres of high value cover types and associated habitats (e.g., adjacent 27 riparian or other woodlands, roadside tree rows, hedge rows, wetlands, etc.) that occur within the 28 agricultural matrix. While there will be an approximate 8 percent net reduction in the extent of 29 agricultural lands in the Plan Area resulting primarily from the restoration of tidal communities, 30 the BDCP would increase the amount of agricultural land under protected status from 11 percent 31 to between 15 and 18 percent (Table 5-2). A sufficient extent agricultural land providing habitat 32 values for covered and other wildlife species, however, will be protected and enhanced at each of 33 the evaluation points to address any temporal loss of habitat functions and to contribute to the 34 conservation of agricultural land-associated covered and other native species. 35

Agricultural land protection could occur in all Conservation Zones; however, conservation 36 efforts would be directed geographically in order to meet the objectives for individual covered 37 species, including greater sandhill crane, Swainson’s hawk, and giant garter snake. BDCP-38 managed agricultural lands are expected to support higher habitat functions for associated 39



covered species by farming crop types that provide high habitat values for covered and other 1 native wildlife species and, where possible, enhancing patches of native habitat within the 2 agricultural landscape. Because the value of agricultural lands is highly variable and fluid, 3 protected acres were calculated based on an analysis of habitat/cover type value and a conversion 4 to habitat units. Of the 503,799 acres of agricultural land within the Plan Area, approximately 5 155,000 acres (31 percent) is considered moderate to high value for covered species. Thus, the 6 management of BDCP-protected lands as high value agricultural habitat can successfully offset 7 the overall reduction in the extent of agricultural lands across the landscape and meet the habitat 8 objectives for each agricultural-associated covered species. In addition, the restoration of tidal 9 and nontidal marshes, riparian forests and scrub, and grasslands with the agricultural matrix 10 would enhance the overall ecological value of the adjacent agricultural lands. 11

5.4.3 Covered Wildlife and Plant Species 12

The following summarizes the overall effects of implementing the BDCP actions on each of the 13 covered wildlife and plant species. The extent of each covered wildlife and plant species’ habitat 14 that would be permanently and temporarily removed and periodically affected by BDCP at the 15 late long-term evaluation point are presented in Table 5-3. The table also indicates the total 16 extent of each species’ habitat types that will be present in the Plan Area following full 17 implementation of the BDCP. The extent of habitat benefits provided through implementation of 18 conservation measures to protect and enhance existing habitats and restore new habitat areas for 19 each of the covered wildlife and plant species following full BDCP implementation are presented 20 in Table 5-4. 21

The complete effects analysis will present the permanent, temporary, and periodic effects on 22 each species for each of the evaluation periods for the entire Plan Area and each of the 11 Plan 23 Area Conservation Zones (Figure 3-1) and will describe the combined effects of implementing 24 all BDCP actions for each of the covered wildlife and plant species at the near-term, early long-25 term, and late long-term evaluation periods. The mechanisms associated with each of the BDCP 26 actions that can result in a permanent or temporary direct or indirect effect or periodic effect on 27 each of covered wildlife and plant species will also be described and evaluated in the full effects 28 analysis. 29

5.4.3.1 San Joaquin Kit Fox 30

Implementation of all BDCP actions will result in an overall benefit to San Joaquin kit fox within 31 the Plan Area and adjacent areas though a directed process of protecting the highest functioning 32 grassland supporting kit fox breeding habitat both intrinsically and in association with other 33 habitat types and habitat corridors and managing protected grasslands to maximize their 34 ecological functions. The BDCP will protect and enhance 1,000 acres kit fox grassland breeding 35 and foraging habitat in Conservation Zone 8 and protect and increase connectivity of its limited 36 Plan Area habitats with extensive kit fox habitat areas outside of the Plan Area. Protected habitat 37 will be managed to enhance rodent prey availability for the kit fox. Following implementation, 38



31 percent of kit fox breeding habitat within the Plan Area will be protected, increasing the total 1 area of protected breeding habitat by 144 percent (Table 5-4). In addition, any portion of the 2 2,000 acres of BDCP restored grassland that is located in Conservation Zone 8 would also be 3 expected to benefit the kit fox. 4

All protection of kit fox habitat would be provided in and all adverse effects on San Joaquin kit 5 fox habitat would be incurred in the near-term evaluation period. Permanent adverse effects on 6 San Joaquin kit fox from implementing BDCP actions include the loss of 163 acres of grassland 7 breeding and 663 acres of adjacent agricultural movement habitat (Table 5-3). Temporary 8 adverse effects include the temporary removal of 161 acres of grassland and 481 acres of 9 adjacent agricultural land, which are expected to be restored following the completion of water 10 conveyance construction (Table 5-3). In contrast to the removed grassland habitats, the 11 grasslands to be protected and enhanced occur in areas of historical natural grassland vegetation. 12

5.4.3.1.1 Population-Level Effects on San Joaquin Kit Fox 13 BDCP actions are not expected to have an adverse or beneficial population-level effect on San 14 Joaquin kit fox in the near-term, early long-term, or late long-term evaluation points because 15 species abundance within the Plan Area is considered to be low based on recent data and 16 modeled habitat and because removed habitat is typically low value. There are very few recent 17 records of San Joaquin kit fox from anywhere within its northern range of Alameda and Contra 18 Costa counties. Modeled kit fox habitat to be removed by BDCP actions is low value, highly 19 disturbed, and fragmented from intact grasslands to the west, and occurs on the extreme edge of 20 the species range. Effects associated with implementation of BDCP actions therefore are not 21 expected to adversely affect the regional San Joaquin kit fox population. 22

5.4.3.2 Riparian Woodrat 23

Implementation of all BDCP actions will result in an overall potential benefit to riparian woodrat 24 within the Plan Area through protection and restoration of its habitat. The BDCP will restore 25 5,000 acres of riparian habitat, approximately 4,000 of which will be in Conservation Zone 7. A 26 substantial portion of this is expected to provide high value riparian habitat for the riparian 27 woodrat without implementing site-specific enhancement actions. However, because the extent 28 of high value habitat cannot be quantified, BDCP will also directly restore 300 acres to meet the 29 ecological and habitat requirements of the riparian woodrat in Conservation Zone 7 or 8. 30 Restoration of 300 acres of riparian habitat will increase the extent of available habitat for the 31 riparian woodrat in the Plan Area by 18 percent and increase the number of protected areas by 32 306 percent (Table 5-3 and 5-4). The actual increase in available and protected acres is expected 33 to be substantially higher due to the overall extent of riparian restoration. 34

The species is not known to occur in the Plan Area and thus is not expected to be affected by 35 BDCP actions unless the species were to establish in the Plan Area over the term of the BDCP. 36 BDCP actions that affect riparian woodrat modeled habitat consist only of floodplain restoration 37 and protection and management of natural communities. BDCP actions are projected to 38



permanently remove 25 acres, temporarily remove 14 acres, and periodically inundate 98 acres 1 of modeled woodrat habitat, respectively. The majority of these acres would not be affected until 2 the late-long term and would be addressed by ongoing riparian habitat restoration. 3

5.4.3.2.1 Population-Level Effects on Riparian Woodrat 4 BDCP actions will not have an adverse population-level effect on riparian woodrat because it is 5 not currently present in the Plan Area and will not be affected by BDCP actions unless the 6 riparian woodrat were to establish in the Plan Area before full BDCP implementation. 7 Implementation of actions to restore 5,000 acres of riparian habitat, 300 of which will be restored 8 specifically to meet the habitat requirements of the riparian woodrat is expected to provide a 9 population-level benefit by providing habitat to accommodate the expansion of existing 10 populations near the Plan Area, increase its distribution and abundance, and reduce the risk for 11 its extinction. 12

5.4.3.3 Salt Marsh Harvest Mouse 13

Implementation of all BDCP actions will result in an overall benefit to salt marsh harvest mouse 14 within the Plan Area through restoration and enhancement of its habitat. Based on the RMA 15 hypothetical tidal habitat restorations (see Appendix N3, RMA Description of Hypothetical 16 Restoration Design and Effects), 3,600 to 4,800 acres of tidal brackish wetlands supporting salt 17 marsh harvest mouse habitat will be restored in Suisun Marsh (Conservation Zone 11; Table 5-18 3). BDCP actions are expected to adversely affect salt marsh harvest mouse habitat through the 19 permanent removal of 2,487 acres of modeled wetland habitat and 674 acres of modeled upland 20 habitat (Table 5-3). However, this effect will be gradual and phased over time as restoration is 21 occurring. Tidal wetlands will be restored in large patches supporting a natural gradient 22 extending from subtidal to upland zones which is expected to increase the extent of high value 23 tidal marsh that supported the salt marsh harvest mouse’s historical tidal habitat and help achieve 24 the draft Tidal Marsh Ecosystems Recovery Plan (USFWS 2010) salt marsh harvest mouse 25 objectives. The enhancement and restoration of 350-700 acres of upland habitat adjacent to 26 restored marshes are expected to provide high functioning flood refuge habitat for the mouse. 27 Based on the hypothetical tidal marsh restorations, (see Appendix N3, RMA Description of 28 Hypothetical Restoration Design and Effects), after full implementation of the BDCP there will 29 be a 10 to 21 percent increase in the extent of salt marsh harvest mouse habitat in the Plan Area. 30 The extent of existing protected salt marsh harvest mouse tidal wetland habitat is expected to 31 increase to 13 to 25 percent (Table 5-4). 32

5.4.3.3.1 Population-Level Effects on Salt Marsh Harvest Mouse 33

Salt marsh harvest mouse are restricted to natural saline and brackish wetlands along the 34 northern borders of San Pablo and Suisun Bays and BDCP conservation measures are expected 35 to have a beneficial effect on the overall population of salt marsh harvest mouse by increasing 36 the extent of tidal brackish wetlands that support high function salt marsh harvest mouse habitat. 37 Restoration and subsequent management of this habitat is expected to provide the basis for 38



increasing the abundance of salt marsh harvest mouse such that the Suisun Marsh portion of its 1 population is maintained and increased. 2

5.4.3.4 Riparian Brush Rabbit 3

Implementation of all BDCP actions will result in an overall potential benefit to riparian brush 4 rabbit within the Plan Area through protection and restoration of its habitat. The BDCP will 5 restore 5,000 acres of riparian habitat, approximately 4,000 of which will be in Conservation 6 Zone 7. A substantial portion of this is expected to provide high value riparian habitat for the 7 riparian brush rabbit without implementing site-specific enhancement actions. However, 8 because the extent of high value habitat cannot be quantified, BDCP will also directly restore 9 300 acres to meet the ecological and habitat requirements of the riparian brush rabbit in 10 Conservation Zone 7. Restoration of 300 acres of riparian habitat will increase the extent of 11 available habitat for the riparian brush rabbit in the Plan Area by 8 percent and increase the 12 number of protected acres by 215 percent (Table 5-4). The actual increase in available and 13 protected acres is expected to be substantially higher due to the overall extent of riparian 14 restoration. 15

BDCP actions that affect riparian brush rabbit modeled habitat consist of water conveyance 16 construction, floodplain restoration, and protection and management of natural communities. 17 None of the affected habitat areas are currently known to be occupied by riparian brush rabbit. 18 BDCP actions are projected to permanently remove 62 acres, temporarily remove 19 acres, and 19 periodically inundate 264 acres of modeled brush rabbit habitat, respectively (Table 5-4). The 20 majority of these acres would not be affected until the late-long term and would be offset by 21 ongoing riparian restoration. 22

5.4.3.4.1 Population-Level Effects on Riparian Brush Rabbit 23 BDCP actions will not have an adverse population level effect on riparian brush rabbit because 24 affected areas are not currently occupied by brush rabbit populations. BDCP actions may benefit 25 the riparian brush rabbit by providing potential habitat for future population expansion in the 26 early long-term and late long-term implementation periods. Restoration of 5,000 acres of 27 riparian habitat, 300 acres of which will be restored specifically to meet the habitat requirements 28 of the riparian brush rabbit habitat is expected to provide a population-level benefit by providing 29 habitat to accommodate the expansion of existing populations in the Plan Area, increase its 30 distribution and abundance, and reduce the risk for its extinction. 31

5.4.3.5 Townsend’s Big-eared Bat 32

Implementation of BDCP actions will result in an overall benefit to Townsend’s big-eared bat 33 within the Plan Area through protection and restoration of its foraging and roosting habitats. 34 BDCP actions will restore 5,000 acres of riparian roosting and primary foraging habitat, 35 2,600 acres of grassland, vernal pool complex, and nontidal marsh foraging habitat, up to 36 65,000 acres of tidal wetland foraging habitat, and protect 8,000 acres of grassland and up to 37



32,640 acres of agricultural foraging habitat. Restoration actions will increase the extent of 1 primary foraging and roosting habitat for the Townsend’s big-eared bat by 69 percent and 2 increase the overall number of protected acres of foraging and roosting habitat by 258 percent 3 (Table 5-4). Restored foraging habitats replace primarily agricultural lands. Restored habitats 4 are expected to be of higher function because the production of flying insect prey species is 5 expected to be higher in restored wetlands and uplands on which application of pesticides will be 6 reduced relative to affected agricultural habitats. 7

All BDCP actions will affect Townsend’s big-eared bat modeled habitat; however, BDCP 8 actions are expected to increase the habitat value of the majority of affected acres. BDCP 9 actions are expected to permanently convert 860 acres of primary foraging habitat, nearly all of it 10 due to tidal habitat restoration, to other types of foraging habitat. They are also expected to 11 remove 268 acres of roosting and primary foraging habitat and convert 60,051 acres of 12 secondary foraging habitat (primarily agricultural land) in the Plan Area to other foraging habitat 13 types (Table 5-3). The majority of affected acres will convert agricultural land to natural 14 communities with higher potential foraging and roosting value, such as riparian, tidal and non-15 tidal wetlands, and periodically inundated lands. Temporary effects on the Townsend’s big-16 eared bat are comparatively small, affecting only 76 acres of primary foraging habitat, 86 acres 17 of roosting and primary foraging habitat, and 4,592 acres of secondary foraging habitat (Table 18 5-3). BDCP actions are expected to periodically convert 291 acres of modeled primary foraging 19 habitat, 301 acres of modeled roosting/primary foraging habitat, and 30,619 acres of modeled 20 secondary foraging habitat to seasonally inundated foraging habitat. Similar to permanent 21 habitat impacts, most temporary and periodic impacts convert existing habitat to higher value 22 habitat and enhance the foraging and roosting functions of BDCP lands for Townsend’s big-23 eared bat. 24

5.4.3.5.1 Population-Level Effects on Townsend’s Big-Eared Bat 25 BDCP actions will not have an adverse population-level effect on Townsend’s big-eared bat 26 because the species is not known to roost and is otherwise uncommon in the Plan Area and 27 because most BDCP actions will enhance habitat function and value for this species. While there 28 will be a temporal loss of primary riparian roosting and foraging habitat (Section 5.4.2.5, 29 Valley/Foothill Riparian), the availability of this habitat in the Plan Area likely exceeds the 30 current habitat need based on the lack of documented occurrences of this species in the Plan Area 31 and surrounding lands. The protection, restoration, and enhancement of 5,000 acres of 32 Townsend’s big-eared bat roosting and primary foraging habitat by the late-long term period 33 along with the conversion of agricultural lands to higher value foraging habitat is expected to 34 sustain any Townsend’s big-eared bat population, were it to establish in the Plan Area. 35

5.4.3.6 Suisun Shrew 36

Implementation of all BDCP actions will result in an overall benefit to Suisun shrew within the 37 Plan Area resulting from a net increase in the extent and contiguity of high value historical 38 Suisun shrew tidal habitat. Based on the RMA hypothetical tidal habitat restorations 39



(see Appendix N.3, RMA Description of Hypothetical Restoration Design and Effects), 3,600 to 1 4,800 acres of tidal brackish wetlands supporting Suisun shrew habitat will be restored in Suisun 2 Marsh (Conservation Zone 11; Table 5-3). BDCP actions are expected to adversely affect 3 Suisun shrew habitat through the permanent removal of 6,237 acres of modeled habitat, 4 consisting primarily of managed wetlands (Table 5-3); however, this effect will be gradual and 5 phased over time as restoration is occurring. Tidal wetlands will be restored in large patches 6 supporting a natural gradient extending from subtidal to upland zones which is expected to 7 increase the extent of high value tidal marsh that supported the Suisun shrew’s historical tidal 8 habitat and help achieve the draft Tidal Marsh Ecosystems Recovery Plan (USFWS 2010) 9 Suisun shrew objectives. Based on the hypothetical tidal marsh restorations, (see Appendix N.3, 10 RMA Description of Hypothetical Restoration Design and Effects), after full implementation of 11 the BDCP there will be a 5 to 9 percent reduction in the extent of Suisun shrew habitat in the 12 Plan Area (Table 5-3), comprised primarily of low value Suisun shrew managed wetland habitat. 13 Because restored tidal wetland habitats are expected to support higher functions as habitat for the 14 Suisun shrew than the affected nontidal wetlands, the overall outcome for Suisun shrew will be 15 beneficial, providing conditions favorable for increasing the distribution and abundance of 16 Suisun shrew within the Plan Area. 17

5.4.3.6.1 Population-Level Effects on Suisun Shrew 18 Since Suisun shrew are restricted to natural tidal wetlands along the northern borders of San 19 Pablo and Suisun Bays and BDCP conservation measures are expected to have a beneficial effect 20 on the overall population of Suisun shrew by increasing the extent of tidal brackish emergent 21 wetlands that support high function Suisun shrew habitat. Restoration and subsequent 22 management of this habitat are expected to provide the basis for increasing the abundance of 23 Suisun shrew such that the Suisun Marsh portion of its population is maintained and increased. 24

5.4.3.7 Tricolored Blackbird 25

Implementation of all BDCP actions will result in an overall benefit to tricolored blackbird 26 within the Plan Area through restoration and protection of its foraging and nesting habitats. 27 Habitat restoration actions will result in restoration/creation of 17,900 to 26,800 acres of 28 tricolored blackbird nesting habitat (based on the RMA hypothetical tidal habitat restorations 29 presented in Appendix N3, RMA Description of Hypothetical Restoration Design and Effects), 30 and after full implementation of the BDCP, 8,700 acres of non-agriculture foraging habitat and 31 16,620 to 32,640 acres of agriculture foraging habitat will be protected and enhanced for 32 tricolored blackbird and other covered species. As a result of BDCP restoration actions, the total 33 amount of tricolored blackbird nesting habitat within the Plan Area will increase 57 to 94 percent 34 from current conditions (Table 5-4). While the extent of modeled foraging habitat will be 35 reduced by 6 percent (non-agricultural) and 9 percent (agricultural), tricolored blackbirds may 36 also use the restored tidal and nontidal wetland habitats for foraging, a function that was not 37 included in the model formulation (Table 5-3). As a result, implementation of all BDCP actions 38 is expected to result in an overall beneficial effect on tricolored blackbird as BDCP 39 implementation will increase the extent of protected nesting and agricultural and non-agricultural 40



foraging habitats in the Plan Area that will no longer be subject to loss that could result from 1 future changes in land use by 101 to 163 percent, 12 percent, and 43 to 91 percent, respectively, 2 from current conditions (Table 5-4). In addition, restoration of large and contiguous protected 3 patches of nesting habitat is expected to increase the likelihood for increasing the number and 4 distribution of nesting colonies and the abundance of tricolored blackbirds in the Plan Area. 5

Implementation of BDCP actions is expected to result in the permanent removal of 6 approximately 4,104 acres of modeled nesting habitat, 5,878 acres of non-agriculture foraging 7 habitat, and 24,781 acres of agriculture foraging habitat (Table 5-3). Approximately 35 acres of 8 nesting habitat, 471 acres of non-agriculture foraging habitat, and 1,959 acres of agriculture 9 foraging habitat will be temporarily removed. An additional 303 acres of nesting habitat, 10 5,414 acres of non-agriculture foraging habitat, and 6,599 acres of agriculture foraging habitat 11 will be periodically affected by BDCP actions. 12

5.4.3.7.1 Population-Level Effects on Tricolored Blackbird 13 BDCP actions will not have an adverse population level effect on the tricolored blackbird 14 because protection, restoration, and enhancement of a large extent of tricolored blackbird habitat 15 within the Plan Area is expected to increase the stability of tricolored blackbird populations 16 within and adjacent to the Plan Area and provide for the potential future growth of the local and 17 regional populations. 18

5.4.3.8 Suisun Song Sparrow 19

Implementation of all BDCP actions will result in an overall benefit to Suisun song sparrow 20 within the Plan Area through restoration of its habitat. Based on the RMA hypothetical tidal 21 habitat restorations (see Appendix N.3, RMA Description of Hypothetical Restoration Design 22 and Effects), 3,600 to 4,800 acres of tidal brackish wetlands supporting Suisun song sparrow 23 habitat will be restored in Suisun Marsh (Conservation Zone 11; Table 5-2). BDCP actions are 24 expected to adversely affect Suisun song sparrow through the permanent removal of 5,272 acres 25 of modeled habitat, consisting primarily of managed wetlands (see Table 5-3). However, this 26 effect will be gradual and phased over time as restoration is occurring. Tidal wetlands will be 27 restored in large patches supporting a natural gradient extending from subtidal to upland zones 28 which is expected to increase the extent of high value tidal marsh that supported the sparrow’s 29 historical tidal habitat and help achieve the draft Tidal Marsh Ecosystems Recovery Plan 30 (USFWS 2010) Suisun song sparrow objectives. 31

Based on the hypothetical tidal marsh restorations, (see Appendix N3, RMA Description of 32 Hypothetical Restoration Design and Effects), after full implementation of the BDCP there will 33 be a 2-6 percent reduction in the extent of Suisun song sparrow habitat in the Plan Area 34 (Table 5-3), comprised primarily of low value Suisun song sparrow managed wetland habitat. 35 Because tidal habitat restoration in Conservation Zone 11 will affect primarily managed wetland 36 habitats, many of which are protected through conservation easements, the extent of existing 37 protected Suisun song sparrow habitat is expected to decrease by up to 6 percent (Table 5-4). 38



Because restored tidal wetland habitats are expected to support higher functions as habitat for the 1 Suisun song sparrow than the affected nontidal wetlands, the overall outcome for Suisun song 2 sparrow will be beneficial, providing conditions favorable for increasing the distribution and 3 abundance of Suisun song sparrow within the Plan Area. 4

5.4.3.8.1 Population-Level Effects on Suisun Song Sparrow 5 BDCP actions will not have an adverse population-level effect on Suisun song sparrow in the 6 near-term, early long-term, or late-long term evaluation points because affected habitat in Suisun 7 Marsh will be sequenced with habitat restoration activities to minimize adverse effects on habitat 8 that could affect that population. Because the entire population of Suisun song sparrow is found 9 within the Plan Area, BDCP tidal habitat restoration actions are expected to be beneficial for the 10 entire Suisun song sparrow population by replacing marginal managed wetland habitat with high 11 quality tidal habitat, and thus creating the potential for extending the species abundance and 12 distribution. 13

5.4.3.9 Yellow-breasted Chat 14

Implementation of all BDCP actions is expected to result in an overall benefit to yellow-breasted 15 chat within the Plan Area through restoration of 5,000 acres of its riparian habitat of which at 16 least 2,000 acres is expected to support vireo habitat. BDCP actions are expected to result in the 17 permanent and temporary removal of up to 1,049 acres and 129 acres of modeled yellow-18 breasted chat habitat, respectively (Table 5-3), primarily due to tidal marsh restoration actions, 19 although the affected habitat is not known to be occupied. Restoration of 5,000 acres of riparian 20 habitat is expected to increase the extent of yellow-breasted chat habitat in the Plan Area by 21 4,087 acres, or 28 percent, and the extent of chat habitat under protected status within the Plan 22 Area is expected to increase by about 85 percent (Tables 5-3 and 5-4). Most of this restored 23 valley/foothill riparian will be in large patches associated with restored floodplain and tidal 24 habitats. The restoration of such a large area of riparian forest and scrub increases the potential 25 for increasing the abundance and distribution of nesting yellow-breasted chat in the Plan Area 26 and is expected to improve the function of the Plan Area as a migration corridor. As described in 27 Section 5.4.2.5, Valley/Foothill Riparian, there is a temporal loss of riparian habitat in the near-28 term evaluation period because most of the affected riparian vegetation is removed in the near-29 term implementation period, while large quantities of riparian habitat will not be restored until 30 the early and late long-term implementation periods (Figures 5-3 and 5-5). Effects on yellow-31 breasted chat of this temporal loss of riparian vegetation is expected to be minimal because much 32 of the riparian habitat in the Plan Area is not known to be currently occupied by the species and 33 most of the affected community is comprised of small patches of riparian scrub and herbaceous 34 vegetation that are fragmented and distributed across the agricultural landscape of the Plan Area 35 (Figure 5-4) and thus are likely to provide no or low value habitat for the chat. 36

In summary, the yellow-breasted chat is not an established breeder within the Plan Area and 37 seems to use the area as an infrequent migrant. Consequently, BDCP actions are unlikely to 38 adversely affect the species. The overall effect of implementing BDCP actions on yellow-39



breasted chat is expected to be beneficial as a result of increasing the extent of riparian forest and 1 scrub that supports high-functioning yellow-breasted chat habitat. Restoration and subsequent 2 management of this habitat will provide the basis for increasing the abundance of yellow-3 breasted chat such that its population is maintained and increased. 4

5.4.3.9.1 Population-Level Effects on Yellow-breasted Chat 5 Because yellow-breasted chat is not known to be established in the Plan Area, BDCP actions are 6 not expected to have any adverse population-level effect on yellow-breasted chat populations. 7 BDCP riparian habitat restoration actions are expected to be beneficial for yellow-breasted chat 8 by creating the potential for extending the species occupied range and providing habitat that, if 9 yellow-breasted chat becomes established as a breeding species, could provide a source 10 population for establishment of other historically occupied Central Valley habitats. 11

5.4.3.10 Least Bell’s Vireo 12

Implementation of all BDCP actions is expected to result in an overall benefit to yellow-breasted 13 chat within the Plan Area through restoration of 5,000 acres of riparian vegetation of which at 14 least 2,000 acres is expected to support vireo habitat. Implementation of BDCP actions is 15 expected to result in the permanent and temporary removal of up to 1,049 acres and 129 acres, 16 respectively of modeled least Bell’s vireo habitat (Table 5-3), primarily due to tidal marsh 17 restoration actions. Although least Bell’s vireo were observed in the Plan Area in spring 2010, it 18 is not known to currently occupy habitat within the Plan Area, therefore effects are evaluated 19 based on the potential removal or restoration of modeled habitat and some potential for future 20 occupation. Restoration of at least 2,000 acres of riparian forest and scrub that is expected to 21 support least Bell’s vireo habitat will increase the extent of potential least Bell’s vireo habitat in 22 the Plan Area by approximately 1,092 acres, or 7 percent, and the extent of vireo habitat under 23 protected status within the Plan Area is expected to increase to more than 25 percent (Tables 5-3 24 and 5-4). Most of this restored valley/foothill riparian will be in large patches associated with 25 restored floodplain and tidal habitats. The restoration of such a large area of riparian forest and 26 scrub increases the potential for restoring formally occupied habitat by establishing the least 27 Bell’s vireo as a breeding species within the Plan Area. As described in Section 5.4.2.5, 28 Valley/Foothill Riparian, there is a temporal loss of riparian habitat in the near-term evaluation 29 period because most of the affected riparian vegetation is removed in the near-term 30 implementation period, while large quantities of riparian habitat will not be restored until the 31 early and late long-term implementation periods (Figures 5-3 and 5-5). This temporal loss is 32 expected to have no or minimal effects on least Bell’s vireo because it is not currently known to 33 occupy the Plan Area. 34

In summary, the least Bell’s vireo is not an established breeder within the Plan Area, and BDCP 35 actions are unlikely to adversely affect the species. The overall effect of implementing BDCP 36 actions on least Bell’s vireo is expected to be beneficial as a result of increasing the extent of 37 riparian forest and scrub that supports higher-functioning least Bell’s vireo habitat. Restoration 38



and subsequent management of this habitat will to provide the basis for increasing the range of 1 least Bell’s vireo by establishing it as a breeding species in the Plan Area. 2

5.4.3.10.1 Population-Level Effects on Least Bell’s Vireo 3 Because least Bell’s vireo is not known to be established in the Plan Area, BDCP actions are not 4 expected to have an adverse population-level effect on least Bell’s vireo populations. Overall, 5 BDCP riparian habitat restoration actions are expected to be beneficial for least Bell’s vireo by 6 creating the potential for extending the species occupied range northward. By restoring at least 7 2,000 acres of riparian forest and scrub habitat, BDCP will provide habitat that, if least Bell’s 8 vireo becomes established as a breeding species, could support a source population for 9 establishment of other historically occupied Central Valley habitats. 10

5.4.3.11 Western Burrowing Owl 11

Implementation of BDCP actions are expected to result in an overall benefit to the burrowing 12 owl in the Plan Area through restoration, protection, and management of its habitat. The BDCP 13 will restore 2,000 acres and protect 8,000 acres of high value grassland habitat within 14 Conservation Zones 1, 8, and 11; and of the 12,000 to 28,000 acres of non-rice agricultural lands 15 that will be protected, 3,000 acres will target moderate and high value (pastureland and 16 grassland) burrowing owl habitats, for a total of 13,000 acres of high and moderate value 17 burrowing owl habitat restored and/or protected in the Plan Area. Through these actions, 18 protection of high and moderate value habitats for burrowing owl will increase by 31 percent and 19 at least 18 percent, representing a total of 45 percent and 40 percent of protected modeled high 20 and moderate value habitat in the Plan Area, respectively (Table 5-4). 21

BDCP actions are expected to adversely affect burrowing owl through the permanent removal or 22 conversion of 3,569 acres of modeled high value habitat and 4,260 acres of moderate-value 23 habitat. The largest extent of habitat conversion, 21,631 acres, is low value (agricultural land) 24 habitat (Table 5-3). An additional 410 acres of high value habitat and 46 acres of moderate value 25 habitat will be removed temporarily and 2,923 acres of high value habitat and 1,651 acres of 26 moderate value habitat will be periodically affected. Similarly, the largest extent of temporary 27 and periodic habitat effects is low value habitat, 1,970 and 10,265 acres, respectively (Table 5-28 3). While the extent of modeled high value and moderate value burrowing owl habitat will be 29 reduced in the Plan Area by 2 percent and 8 percent, respectively, BDCP restoration, protection, 30 and enhancement actions, particularly the increase in protection of high and moderate value 31 habitat in the Plan Area is expected to provide for the protection and future expansion of the 32 burrowing owl population (Table 5-3). 33

5.4.3.11.1 Population-Level Effects on Burrowing owl 34 BDCP actions will not have an adverse population-level effect on burrowing owl in the Plan 35 Area. The Plan Area represents only a small fraction of the known distribution of burrowing 36 owls in California. The protection, restoration, and enhancement of 13,900 acres of burrowing 37 owl high and moderate-value habitat associated with BDCP action is expected to at least sustain 38



burrowing owl numbers within and adjacent to the Plan Area and increase the permanent 1 protection of high quality habitat for the species. 2

5.4.3.12 Western Yellow-Billed Cuckoo 3

Implementation of all BDCP actions is expected to result in an overall benefit to western yellow-4 billed cuckoo within the Plan Area through restoration of restoration of 5,000 acres of riparian 5 vegetation of which at least 1,000 acres is expected to support cuckoo habitat. BDCP actions are 6 expected to result in the permanent and temporary removal of up to 574 acres and 228 acres of 7 modeled yellow-billed cuckoo breeding and migratory habitat, respectively (Table 5-3), 8 primarily due to tidal marsh restoration actions. The western yellow-billed cuckoo is not known 9 to currently occupy habitat within the Plan Area, therefore effects are evaluated based on the 10 potential removal or restoration of modeled habitat and some potential for future occupation. 11 Restoration of at least 1,000 acres of riparian forest is expected to increase the extent of western 12 yellow-billed cuckoo breeding habitat in the Plan Area by at least 426 acres. A large proportion 13 of the remaining 4,000 acres of the 5,000 acres of riparian forest and scrub to be restored under 14 the BDCP is expected to develop as breeding or migratory western yellow-billed cuckoo. 15

Most of this restored valley/foothill riparian will be in large patches, as opposed to the primarily 16 smaller isolated patches of affected habitat, associated with restored floodplain and tidal habitats. 17 The restoration of such a large area of riparian forest and scrub increases the potential for 18 restoring formally occupied habitat by establishing western yellow-billed cuckoo as a breeding 19 species within the Plan Area. As described in Section 5.5.2.5, Valley/Foothill Riparian, there is 20 a temporal loss of riparian habitat in the near-term evaluation period because most of the affected 21 riparian vegetation is removed in the near-term implementation period, while large quantities of 22 riparian habitat will not be restored until the early and late long-term implementation periods 23 (Figures 5-3 and 5-5). This temporal loss is expected to have no or minimal effects on western 24 yellow-billed cuckoo because it is not currently known to occupy the Plan Area. 25

In summary, the yellow-billed cuckoo is not an established breeding species within the Plan Area 26 and seems to use the area as an infrequent migrant. BDCP actions are unlikely to adversely 27 affect the species. The overall effect of implementing BDCP actions on western yellow-billed 28 cuckoo will be beneficial as a result of increasing the extent of riparian forest that supports high-29 functioning western yellow-billed cuckoo habitat. Restoration and subsequent management of 30 this habitat are expected to provide the basis for increasing the range of western yellow-billed 31 cuckoo by increasing the potential for establishing it as a breeding species in the Plan Area. 32

5.4.3.12.1 Population-Level Effects on Yellow-billed Cuckoo 33 Because western yellow-billed cuckoo is not known to be established in the Plan Area, BDCP 34 actions are not expected to have any adverse population-level effect on western yellow-billed 35 cuckoo. BDCP riparian habitat restoration actions are expected to be beneficial for western 36 yellow-billed cuckoo by creating the potential for extending the species occupied range and 37 providing habitat that, if western yellow-billed cuckoo becomes established as a breeding 38



species, could provide a source population for establishment of other historically occupied 1 Central Valley habitats. 2

5.4.3.13 California Least Tern 3

Implementation of the BDCP will result in overall beneficial effects on California least tern 4 through restoration of an estimated 10,000 to 20,000 acres of its tidal aquatic foraging habitat, 5 increasing its foraging habitat area by 11 to 23 percent. Implementation of BDCP actions will 6 avoid direct disturbance of California least tern nesting colonies and, compared to the extent of 7 restored habitat, will remove a relatively small about of its tidal aquatic foraging habitat (Table 8 5-3). Restoration of more than of tidal perennial aquatic will result in enhanced habitat function 9 for California least tern by its proximity to restored and existing aquatic and upland habitats in a 10 natural elevation gradient. The overall outcome for California least tern is beneficial due to 11 restoration of foraging habitat. 12

5.4.3.13.1 Population-Level Effects on California Least Tern 13 BDCP actions are not expected to have any adverse effect on California least tern in the Plan 14 Area and, therefore, are not expected to have an adverse population-level effect on California 15 least tern. Only a small fraction of the total California least tern population uses the Plan Area 16 and the Plan Area is not identified as a priority area for conservation action in recovery 17 documents associated with the California least tern. Although BDCP actions are expected to 18 increase the extent of shallow subtidal aquatic California least tern foraging habitat and, 19 potentially increase aquatic food production, the response of the tern to these habitat 20 improvements may be minimal because they do not address major known stressors on the 21 species. 22

5.4.3.14 Greater Sandhill Crane 23

Implementation of all BDCP actions will result in an overall benefit to greater sandhill crane 24 within the Plan Area through protection and management of high value foraging habitat and 25 restoration of two roost sites Habitat restoration actions will result in restoration/creation of 26 320 acres of greater sandhill crane roosting habitat, and habitat protection actions will protect at 27 least 4,800 acres of high value greater sandhill crane agricultural foraging habitat in 28 Conservation Zones 4, 5, or 6. In addition, the restoration of 7,100 acres of tidal freshwater 29 wetlands in Conservation Zones 4 and 7 will provide additional roosting and foraging habitat for 30 cranes. BDCP conservation measures will increase the extent of protected agricultural foraging 31 habitats in the primary use area by at least 4 percent from current conditions (Table 5-4), and 32 protected lands will no longer be subject to loss that could result from future changes in land use. 33 In addition, creation and maintenance of two crane roost sites will help improve the distribution 34 of cranes in the primary use area and ensure the long-term availability of this required and 35 limited habitat, without which cranes could not inhabit the Plan Area. 36



BDCP actions will permanently remove 6,739 acres of modeled greater sandhill crane foraging 1 habitat and temporarily remove 1,318 acres of modeled crane foraging habitat in the Plan Area 2 (Table 5-3) calculated to total 3,971 habitat units. While there will be a net reduction in the 3 extent of modeled winter foraging habitat in the Plan Area of approximately 4 percent 4 (Table 5-3), management of protected agricultural foraging habitat will focus on providing high 5 value crane foraging habitat and will be maintained such that a minimum of 3,971 habitat units 6 are available on conservation lands each year. 7

5.4.3.14.1 Population-Level Effects on Greater Sandhill Crane 8 BDCP actions will not have an adverse population-level effect on greater sandhill crane. 9 Protection, restoration, and enhancement of 5,120 acres of greater sandhill crane foraging and 10 roosting habitat is expected to increase the stability of traditional greater sandhill crane wintering 11 use within and adjacent to the Plan Area and provide for the potential future growth of the local 12 wintering population. 13

5.4.3.15 California Black Rail 14

Implementation of all BDCP actions will result in an overall benefit to California black rail 15 within the Plan Area through restoration of its tidal habitats. Based on the RMA hypothetical 16 tidal habitat restorations (see Appendix N.3, RMA Description of Hypothetical Restoration 17 Design and Effects), 17,500 to 26,400 acres of tidal brackish and freshwater wetlands supporting 18 California black rail habitat will be restored (Table 5-2). BDCP actions are expected to 19 adversely affect California black rail habitat through the permanent and temporary removal of 20 5,949 acres and 4 acres of modeled habitat, respectively, consisting primarily of managed 21 wetlands (Table 5-3). Tidal wetlands will be restored in large patches supporting a natural 22 gradient extending from subtidal to upland zones which is expected to increase the extent of high 23 value tidal marsh that supported the rail’s historical tidal habitat and help achieve the draft Tidal 24 Marsh Ecosystems Recovery Plan (USFWS 2010) California black rail objectives. 25

Based on the hypothetical tidal marsh restorations, (see Appendix N.3, RMA Description of 26 Hypothetical Restoration Design and Effects), after full implementation of the BDCP there will 27 be a 34 to 61 percent increase in the extent of California black rail habitat in the Plan Area 28 (Table 5-3). The extent of existing protected California black rail tidal wetland habitat is 29 expected to increase to 50 to 86 percent (Table 5-4). 30

5.4.3.15.1 Population-Level Effects on California Black Rail 31

BDCP actions are not expected to have an adverse population-level effect on California black 32 rail in the near-term, early long-term, or late-long term because affected habitat in the Delta 33 support very low densities of rail and removal of higher value habitats Suisun Marsh will be 34 sequenced with habitat restoration activities to minimize adverse effects on habitat that could 35 affect that population. Since a significant portion of the entire California black rail population 36 resides in Suisun Marsh, BDCP tidal habitat restoration actions are expected to be beneficial for 37



California black rail by creating the potential for extending the species distribution and 1 abundance in the Delta and its abundance in Suisun Marsh. 2

5.4.3.16 California Clapper Rail 3

Implementation of all BDCP actions will result in an overall benefit to California clapper rail 4 within the Plan Area through restoration of its brackish tidal habitats. Based on the RMA 5 hypothetical tidal habitat restorations (see Appendix N.3, RMA Description of Hypothetical 6 Restoration Design and Effects), 3,600 to 4,800 acres of tidal brackish wetlands supporting 7 California clapper rail will be restored in Suisun Marsh (Conservation Zone 11; Table 5-3). 8 BDCP actions are expected to adversely affect California clapper rail habitat through the 9 permanent removal of 327 acres of its modeled habitat in Suisun Marsh as a result of tidal habitat 10 restoration actions (Table 5-3). However, this effect will be gradual and phased over time as 11 restoration is occurring. Tidal wetlands will be restored in large patches supporting a natural 12 gradient extending from subtidal to upland zones which is expected to increase the extent of high 13 value tidal marsh that supported the rail’s historical tidal habitat and help achieve the draft Tidal 14 Marsh Ecosystems Recovery Plan (USFWS 2010) California clapper rail objectives. Based on 15 the hypothetical tidal marsh restorations, (see Appendix N.3, RMA Description of Hypothetical 16 Restoration Design and Effects), after full implementation of the BDCP there will be a 42 to 57 17 percent increase in the extent of salt marsh harvest mouse habitat in the Plan Area. The extent of 18 existing protected salt marsh harvest mouse tidal wetland habitat is expected to increase to 67 to 19 89 percent (Table 5-4). 20

5.4.3.16.1 Population-Level Effects on California Clapper Rail 21 BDCP actions are not expected to have an adverse population-level effect on California clapper 22 rail in the near-term, early long-term, or late-long term evaluation points because affected habitat 23 in Suisun Marsh will be sequenced with habitat restoration activities to minimize adverse effects 24 on habitat that could affect that population. Because the entire California clapper rail population 25 is restricted to the San Francisco Estuary, BDCP tidal habitat restoration actions are expected to 26 be beneficial for California clapper rail by creating the potential for extending its abundance and 27 distribution in Suisun Marsh, which comprises a sizeable portion of its range and overall 28 population. 29

5.4.3.17 Swainson’s Hawk 30

Implementation of BDCP actions will result in an overall benefit to Swainson’s hawk within the 31 Plan Area through restoration of its nesting and protection and management of its foraging 32 habitats. BDCP protection and enhancement of 20,020 to 36,040 acres of Swainson’s hawk 33 foraging habitat to provide a minimum of 17,758 habitat units will increase the extent and quality 34 of Swainson’s hawk foraging habitat under protected status within the Plan Area (Table 5-4). 35 Restoration of at least 4,000 acres of riparian habitat is expected to increase the extent of 36 Swainson’s hawk nesting habitat in the Plan Area by 3,294 acres (32 percent) and the extent of 37



nesting habitat under protected status within the Plan Area is expected to be increased by 1 108 percent (Tables 5-3 and 5-4). 2

BDCP actions are expected to adversely affect Swainson’s hawk through the temporary and 3 permanent removal of 40,678 acres (17,758 habitat units) of modeled Swainson’s hawk foraging 4 and 844 acres of nesting habitat (Table 5-2). Following full BDCP implementation, the extent of 5 Swainson’s hawk nesting habitat acres will increase by 32 percent and the extent of foraging 6 habitat acres will decrease by approximately 9 percent (Table 5-3). However, the overall effect 7 of implementing BDCP actions on Swainson’s hawk is expected to be beneficial as a result of 8 protecting a large proportion of its foraging habitat in the Plan Area from loss or degradation that 9 could be associated with future changes in land use, providing consistently high value 10 Swainson’s hawk foraging habitat on BDCP lands, restoration of 4,000 acres of nesting habitat 11 that is expected to provide future nesting habitat within the Plan Area, and through enhancement 12 of protected habitats to increase their functions as Swainson’s hawk foraging and nesting habitat 13 over the term of the BDCP. 14

5.4.3.17.1 Population-Level Effects on Swainson’s Hawk 15 BDCP actions will not have an adverse population-level effect on Swainson’s hawk. Through 16 the protection, restoration, and enhancement of 24,020 to 40,040 acres of Swainson’s hawk 17 foraging and nesting habitat, BDCP is expected to sustain the current range and abundance of 18 Swainson’s hawk within the Plan Area and provide for potential increases in Swainson’s hawk 19 abundance and distribution within and adjacent to the Plan Area. 20

5.4.3.18 White-tailed Kite 21

Implementation of BDCP actions will result in an overall benefit to the white-tailed kite within 22 the Plan Area through restoration of its nesting and protection and management of its foraging 23 habitat. BDCP protection and enhancement of 24,620 to 46,040 acres of white-tailed kite 24 foraging habitat to provide a minimum of 21,693 habitat units will increase the extent and quality 25 of white-tailed kite foraging habitat under protected status within the Plan Area by 12-33 percent 26 (Table 5-4). Restoration of at least 4,000 acres of riparian habitat is expected to increase the 27 extent of white-tailed kite nesting habitat in the Plan Area by 3,132 acres, or 23 percent, and the 28 extent of nesting habitat under protected status within the Plan Area is expected to be increased 29 by 76 percent (Tables 5-3 and 5-4). 30

BDCP actions are expected to adversely affect white-tailed kite through the temporary and 31 permanent removal of 47,563 acres (21,693 habitat units) of modeled white-tailed kite foraging 32 habitat and 1,013 acres of nesting habitat (Table 5-3). Following full BDCP implementation, the 33 extent of white-tailed kite nesting habitat will increase by 23 percent and the extent of foraging 34 habitat acres will decrease by approximately 9 percent (Table 5-3). However, the overall effect 35 of implementing BDCP actions on white-tailed kite is expected to be beneficial as a result of 36 protecting a large proportion of its foraging habitat in the Plan Area from loss or degradation that 37 could be associated with future changes in land use, providing consistently high value white-38



tailed kite foraging habitat on BDCP lands, restoration of 4,000 acres of nesting habitat that is 1 expected to provide future nesting habitat within the Plan Area, and through enhancement of 2 protected habitats to increase their functions as white-tailed kite foraging and nesting habitat 3 over the term of the BDCP. 4

5.4.3.18.1 Population-Level Effects on White-tailed Kite 5 BDCP actions will not have an adverse population-level effect on white-tailed kite. Through the 6 protection, restoration, and enhancement of 26,020 to 44,040 acres of white-tailed kite foraging 7 and nesting habitat, BDCP is expected to sustain the current range and abundance of white-tailed 8 kites within the Plan Area and provide for potential increases in white-tailed kite abundance and 9 distribution within and adjacent to the Plan Area. 10

5.4.3.19 Giant Garter Snake 11

Implementation of all BDCP actions will result in an overall benefit to giant garter snake within 12 the Plan Area through implementation of giant garter snake habitat protection, restoration, and 13 enhancement actions. Following full implementation of the BDCP, at least 6,900 acres of 14 aquatic habitat and 7,100 acres of upland habitat will be protected and enhanced for giant garter 15 snake. An additional 13,690 to 22,040 of potential aquatic breeding habitat will be restored 16 through restoration of tidal and nontidal freshwater habitats. There will be a 66 to 108 percent 17 increase in the extent of giant garter snake aquatic breeding, foraging, and movement habitat in 18 the Plan Area (Table 5-3). The extent of existing protected giant garter snake aquatic habitat 19 present in the Plan Area is expected to increase by 354 to 500 percent and the extent of protected 20 giant garter snake upland habitat by 13 percent (Table 5-4). 21

BDCP actions are expected to adversely affect giant garter snake through permanent removal of 22 565 acres of modeled aquatic and 13,713 acres of modeled associated upland habitat; temporary 23 removal of 52 acres of aquatic habitat and 941 acres of upland habitat resulting mainly from 24 water conveyance construction; and periodic inundation of 4,932 acres of aquatic and 25 5,534 acres of upland habitat resulting primarily from periodic seasonal inundation of the Yolo 26 Bypass (Table 5-3). The overall result of BDCP implementation for giant garter snake will be 27 beneficial through expansion and enhancement of habitats associated with core habitat areas 28 within existing populations areas, providing protected habitat corridors to facilitate movement, 29 and by providing conditions that are favorable, relative to the existing condition of primarily 30 cultivated lands, for maintaining, expanding, and increasing the distribution and abundance of 31 giant garter snake within the Plan Area. 32

5.4.3.19.1 Population-Level Effects on Giant Garter Snake 33

BDCP actions will not have an adverse population-level effect on giant garter snake because 34 most affected habitat in the Delta are not believed to be occupied by or support very low 35 densities of giant garter snake. Protection and restoration of giant garter snake habitat may have 36 beneficial population-level effects on giant garter snake by maintaining and improving habitats 37



occupied by the two known subpopulations in the Plan Area and by creating the potential for 1 extending the species distribution and abundance within the Plan Area. 2

5.4.3.20 Western Pond Turtle 3

Implementation of all BDCP actions will result in an overall benefit to western pond turtle within 4 the Plan Area through implementation of western pond turtle habitat protection, restoration, and 5 enhancement actions. Full implementation of BDCP habitat actions will restore 27,900 to 46,800 6 acres of pond turtle aquatic habitat and 5,000 acres of upland nesting and overwintering habitat, 7 and will protect and enhance 4,000 acres of dispersal habitat and at least 5,230 acres of upland 8 nesting and overwintering habitat. The extent of existing protected pond turtle aquatic habitat 9 present in the Plan Area is expected to increase by 76 to 138 percent (Table 5-4) and the extent of 10 protected upland nesting and overwintering habitat by more than 42 percent (Table 5-4). 11

BDCP actions are expected to permanently and temporarily remove or affect 6,013 acres 12 (8 percent), nearly all of it due to tidal habitat restoration in Suisun Marsh (Conservation Zone 13 11; Table 5-2), and 84 acres of aquatic habitat, respectively. Tidal habitat restoration is expected 14 to change existing water quality conditions at Suisun Marsh rather than lead to direct loss of 15 aquatic habitat. Changes in salinity and restoration of tidal flow where currently habitat consists 16 of calm waters of managed freshwater ponds and wetlands could have an adverse effect on the 17 western pond turtle. 18

BDCP actions are also expected to permanently and temporarily remove 51,630 acres and 19 4,680 acres of dispersal and upland nesting and overwintering habitat in the Plan Area (Table 5-20 3). Fremont Weir operations and inundation of restored floodplains are expected to periodically 21 affect western pond turtle 20,912 acres of dispersal habitat and 4,163 acres of upland nesting and 22 overwintering habitat (Table 5-3). 23

Overall, BDCP implementation will increase the extent and distribution of high value aquatic 24 and upland nesting and overwintering habitat for western pond turtle in the Plan Area. While the 25 extent of dispersal habitat is expected to be reduced by approximately 9 percent, this habitat is 26 abundant in the Plan Area (comprised primarily of agricultural lands), not believe to be a factor 27 limiting the turtle, and will be replaced with higher value habitats for western pond turtle. 28

5.4.3.20.1 Population-Level Effects on Western Pond Turtle 29 BDCP actions are not expected to have an adverse or beneficial population-level effect on 30 western pond turtle, although enhancement and restoration of its habitats in the Delta are 31 expected to increase its abundance within the Plan Area. A projected rise in salinity and current 32 velocities in Suisun Marsh could adversely affect the western pond turtle population at that 33 location. The restoration of large amounts of subtidal aquatic habitat in other parts of the Plan 34 Area has the potential to increase western pond turtle population numbers. On the terrestrial 35 side, the protection, restoration, and enhancement of upland nesting and overwintering habitat is 36 expected to be beneficial to the species.. 37



5.4.3.21 California Red-legged Frog 1

Implementation of all BDCP actions will result in an overall benefit to California red-legged frog 2 within the Plan Area through protection and management of at least 1,000 acres its grassland and 3 intermittent stream breeding habitats. The BDCP will protect and enhance these habitats in 4 Conservation Zone 8 and protect and increase connectivity of its limited Plan Area habitats with 5 more extensive California red-legged frog habitat areas outside of the Plan Area. Following 6 implementation, 32 percent of California red-legged frog upland habitat and 6 percent of its 7 breeding within the Plan Area will be protected, increasing the total area of protected breeding 8 habitat and upland habitat by 81 percent and 144 percent, respectively (Table 5-4). In addition, 9 any portion of the 2,000 acres of BDCP restored grassland that is located in Conservation Zone 8 10 would also be expected to benefit the California red-legged frog. 11

All protection of frog habitat would be provided in and all adverse effects on California red-12 legged frog habitat would be incurred in the near-term evaluation period. BDCP actions are 13 expected to adversely affect California red-legged frog through permanent removal of 168 acres 14 of California red-legged frog modeled grassland cover and dispersal and 663 acres of modeled 15 agricultural dispersal habitat. An additional 161 acres of modeled grassland cover and 481 acres 16 of modeled agricultural dispersal habitat will be temporarily removed and restored to their 17 previous habitat condition following the completion of construction activities (Table 5-3). 18

In contrast to the removed grasslands, the grasslands to be protected, enhanced, and restored 19 occur in areas of historical natural grassland vegetation, much of which is within the range of the 20 California red-legged frog. 21

5.4.3.21.1 Population-Level Effects on California Red-legged Frog 22 BDCP actions are not expected to have an adverse or beneficial population-level effect on 23 California red-legged frog because there are few occurrences within the Plan Area and only one 24 site with potential to be affected by proposed project activities. In addition, the relatively small 25 about of modeled grassland habitat that would be removed by the proposed project is on the 26 extreme edge of the species range and based on past and current surveys results is unlikely to be 27 occupied. Although 1,000 acres of high value California red-legged frog habitat will be 28 protected and enhanced under BDCP that is located to maintain connectivity with occupied 29 habitat areas adjacent to the Plan Area, because the Plan Area is located at the margin of the 30 species range, BDCP implementation is not expected to have a measurable beneficial population-31 level effect on California red-legged frog. 32

5.4.3.21.2 Effects on Critical Habitat 33 Designated critical habitat for the California red-legged frog overlaps with the Plan Area along 34 the western edge of Conservation Zone 11. Critical Habitat Unit Sol-1 extends along the west 35 side of Interstate 680 (I-680). Approximately 2,460 acres of Sol-1 occurs within the Plan Area 36 boundary. This area is not expected to be affected by any BDCP actions. All tidal restoration 37 within the Suisun Marsh will occur east of I-680 where the land is currently primarily marshland 38



and managed wetlands. The landscape west of I-680 is primarily higher elevation upland 1 grasslands that will not be directly or indirectly affected through changes in hydrology as a result 2 of restoration activities. Therefore, BDCP actions will not affect critical habitat for the 3 California red-legged frog in Conservation Zone 11. 4

A small amount of designated critical habitat for the California red-legged frog is also present 5 along the western edge of Conservation Zone 8. Critical Habitat Unit CCS-2 extends along the 6 eastern edge of the grassland foothills of Eastern Contra County, approximately 862 acres of 7 which occur within the Plan Area. This area is not expected to be adversely affected by any 8 BDCP actions. All water conveyance construction activities will occur west of the critical 9 habitat boundary with the exception of the proposed 230kV transmission line that extends down 10 the California Aqueduct canal southwest of CCF, but still outside of the critical habitat boundary. 11 Conservation actions to protect and enhance grassland habitat for covered species, including 12 California red-legged frog, in Conservation Zone 8 could include acquisition and enhancement 13 of designated critical habitat for the California red-legged frog, California tiger salamander, and 14 San Joaquin kit fox. Any habitat enhancement actions for these species in designated critical 15 habitat are expected to enhance and not diminish the value of any affected designated critical 16 habitat for conservation of California red-legged frog. 17

5.4.3.22 Western Spadefoot Toad 18

Implementation of all BDCP actions will result in an overall benefit on western spadefoot toad 19 within the Plan Area through protection, enhancement, and restoration of its habitat. BDCP 20 conservation measures will restore 200 acres high value vernal pool complex supporting high 21 value western spadefoot toad breeding habitat and protect and enhance 300 acres of existing 22 breeding and 8,400 acres of upland habitat. These protected habitat areas will be located such 23 that they will maintain and enhance connectivity with more extensive patches of suitable habitat 24 adjacent to the Plan Area. BDCP actions are expected to permanently remove of 48 acres of its 25 modeled breeding habitat and permanently and temporarily remove 464 acres and 169 acres of 26 its modeled upland habitat, respectively (Table 5-3). The extent of western spadefoot toad 27 habitat restored and protected at the near-term and early long-term evaluation points exceeds the 28 extent that will be removed by BDCP actions at those evaluation points. Following full 29 implementation of the BDCP, there will be an increase in 158 acres of western spadefoot toad 30 breeding habitat, representing a 2 percent increase in the Plan Area (Table 5-3), and an increase 31 in the extent of existing protected breeding and upland habitat of 12 percent and 173 percent, 32 respectively (Table 5-4). 33

5.4.3.22.1 Population-Level Effects on Western Spadefoot Toad 34 There are no records of western spadefoot toad within the Plan Area. Because of the small 35 amount of modeled habitat affected and the overall increase in breeding and protected upland 36 habitats, BDCP actions will not have an adverse effect on western spadefoot toad populations 37 and may have a beneficial effect by providing additional opportunities for colonization and 38 protecting habitat corridors between protected aquatic habitats. 39



5.4.3.23 California Tiger Salamander 1

Implementation of all BDCP actions will result in an overall benefit on California tiger 2 salamander within the Plan Area through protection, enhancement, and restoration of its habitat. 3 BDCP conservation measures will restore 200 acres high value vernal pool complex supporting 4 high value California tiger salamander breeding habitat and protect and enhance 300 acres of 5 existing breeding and 8,400 acres of upland habitat. These protected habitat areas will be located 6 such that they will maintain and enhance connectivity with more extensive patches of suitable 7 habitat adjacent to the Plan Area. BDCP actions are expected to permanently remove42 acres of 8 its modeled breeding habitat and permanently and temporarily remove 464 acres and 169 acres 9 of its modeled upland habitat, respectively (Table 5-3). The extent of California tiger 10 salamander habitat restored and protected at the near-term and early long-term evaluation points 11 exceeds the extent that will be removed by BDCP actions at those evaluation points. Following 12 full implementation of the BDCP, there will be an increase in 158 acres of California tiger 13 salamander breeding habitat, representing a 2 percent increase in the Plan Area (Table 5-3), and 14 an increase in the extent of existing protected breeding and upland habitat of 12 percent and 173 15 percent, respectively (Table 5-4). 16

5.4.3.23.1 Population-Level Effects on California Tiger Salamander 17 BDCP actions are not expected to have an adverse or beneficial population-level effect on 18 California tiger salamander because, while several important California tiger salamander 19 populations occur in the vicinity of the Plan Area, only a few records from Conservation Zone 8 20 confirm their presence within the Plan Area. In addition, habitat restoration actions will remove 21 42 acres, or less than 1 percent, of its vernal pool complex breeding habitat, which is most 22 limiting for the species. Although 8,900 acres of high value California tiger salamander breeding 23 and upland habitat will be protected, enhanced, and restored under BDCP that is located to 24 maintain connectivity with potentially occupied habitat areas adjacent to the Plan Area, because 25 the Plan Area is located at the margin of the species range, BDCP implementation is not 26 expected to have a measurable beneficial population-level effect on California tiger salamander. 27

5.4.3.23.2 Effects on Critical Habitat 28 Designated critical habitat for California tiger salamander is present in the Plan Area along the 29 western edge of Conservation Zone 1. Critical Habitat Unit 2 extends along the west side of 30 State Route 113 (SR 113) from the short east-west portion of SR-113 south of Hay Road on the 31 north to Creed Road on the south. Approximately 1,781 acres of Unit 2 occur within the Plan 32 Area. While this area occurs within the Cache Slough Complex, it is not expected to be affected 33 by BDCP tidal habitat restoration actions. As modeled in the hypothetical tidal habitat 34 restorations (see Appendix E21), tidal habitat will be restored approximately 2 miles east of SR-35 113 with some restoration occurring along the Barker and Lindsey Slough channels west to 36 approximately SR-113, and a small amount (0.4 acre) occurring along the Lindsey Slough 37 Channel west of SR-113 into Unit 2. While the actual restoration area my vary from the 38 hypothetical restoration area, because of the existing hydrological transition to a vernal pool 39



grassland west of SR-113, there is little potential for tidal marsh restoration occurring in this area 1 with the possible exception of the Lindsey and Barker Slough channels. Further, because the 2 intent is to protect and enhance vernal pool grassland in the area west of SR-113, conversion of 3 this area to tidal habitats is expected to be avoided. Conservation actions to protect and enhance 4 grassland and vernal pool complex habitat for covered species, including California tiger 5 salamander, in Conservation Zone 1 could include acquisition and enhancement of designated 6 critical habitat for the California tiger salamander, covered vernal pool shrimp species, and 7 vernal pool plant species. Any habitat enhancement actions for these species in designated 8 critical habitat are expected to enhance and not diminish the value of any affected designated 9 critical habitat for conservation of California tiger salamander. 10

5.4.3.24 Lange’s Metalmark Butterfly 11

Implementation of the BDCP will result in overall beneficial effects on Lange’s metalmark 12 butterfly. BDCP actions will have no adverse effect Lange’s metalmark butterfly or its habitat 13 and will result in an overall benefit to the ecological function of its habitat at the Antioch Dunes 14 NWR and at other suitable locations, if present, in the Plan Area where Lange’s metalmark 15 habitat may be protected and enhanced or restored. Habitat enhancement and butterfly 16 propagation programs are expected to maintain and potentially increase the abundance of 17 Lange’s metalmark butterfly. 18

5.4.3.24.1 Population-Level Effects on Lange’s Metalmark Butterfly 19

BDCP support of USFWS restoration and enhancement actions at the Antioch Dunes NWR will 20 have beneficial population-level effects on Lange’s metalmark butterfly. BDCP support will 21 help restore inland dune scrub habitat and augment existing populations of Lange’s metalmark 22 butterfly through a program of captive breeding and release into areas of inland dune scrub plant 23 habitat. Lange’s metalmark butterfly is a subspecies of a widely distributed species and is likely 24 endemic to the Plan Area. Thus, beneficial effects of BDCP actions could affect the range-wide 25 status of Lange’s metalmark butterfly. 26

5.4.3.25 Valley Elderberry Longhorn Beetle 27

Implementation of all BDCP actions is expected to result in an overall benefit to valley 28 elderberry longhorn beetle within the Plan Area through restoration 5,000 acres of its riparian 29 habitat supporting its elderberry host plant. Restoration of riparian habitats would increase the 30 distribution and extent of elderberry shrubs and the beetle’s potential distribution and abundance 31 in the Plan Area. BDCP actions are expected to adversely affect valley elderberry longhorn 32 beetle through permanent removal of 1,722 acres and temporary removal of 352 acres of its 33 modeled habitat (Table 5-3), primarily due to tidal habitat restoration, although the affected 34 habitat is not known to be occupied. Periodic effects (through inundation) of an additional 35 1,286 acres of habitat are associated with floodplain restoration and enhancement actions 36 (Table 5-3), which are expected to have no or minimal adverse effects on the beetle. Full 37 implementation of the BDCP will result in an increase of 3,898 acres, or 23 percent, in the extent 38



of riparian habitat in the Plan Area, much of which will support the host plant for valley 1 elderberry longhorn beetle; and a 42 percent increase in the extent of existing protected habitat in 2 the Plan Area (Table 5-4). 3

As described in Section 5.4.2.5, Valley/Foothill Riparian, there is a temporal loss of riparian 4 habitat in the near-term evaluation period because most of the affected riparian vegetation is 5 removed in the near-term implementation period, while large quantities of riparian habitat will 6 not be restored until the early and late long-term implementation periods (Figures 5-3 and 5-5). 7 Effects on valley elderberry longhorn beetle of this temporal loss of riparian vegetation is 8 expected to be minimal because much of the riparian habitat in the Plan Area is not known to be 9 currently occupied by the species and most of the affected community is comprised of small 10 patches of riparian scrub and herbaceous vegetation that are fragmented and distributed across 11 the agricultural landscape of the Plan Area (Figure 5-4) and thus are likely to provide no or low 12 value habitat for the beetle. 13

5.4.3.25.1 Population-Level Effects on Valley Elderberry Longhorn Beetle 14 BDCP actions will not have an adverse population-level effect on valley elderberry longhorn 15 beetle because BDCP actions will affect less that 5 percent of its modeled habitat, much of which 16 is likely not occupied, and BDCP restoration actions will increase its habitat by 23 percent 17 commensurate or in advance of when habitat will be affected. Increasing the distribution of its 18 habitat and its extent by 23 percent is expected to provide the basis for increasing the abundance 19 and distribution of valley elderberry longhorn beetle in the Plan Area. Depending on where 20 riparian habitats are restored, increasing the extent of riparian habitat is also expected to increase 21 connectivity of its habitat with habitat areas adjacent to the Plan Area, which will help maintain 22 or improve the regional status of the species’ population. 23

5.4.3.26 Vernal Pool Shrimp Species (Vernal Pool Tadpole Shrimp, 24 Conservancy Fairy Shrimp, Longhorn Fairy Shrimp, Vernal Pool 25 Fairy Shrimp, Mid Valley Fairy Shrimp, and California Linderiella) 26

Implementation of all BDCP actions will result in an overall benefit to the vernal pool shrimp 27 species through the restoration of 200 acres of vernal pool complex and the protection and 28 enhancement of 300 acres of existing vernal pool complex. The restored and protected habitat 29 areas will be located such that they will maintain and enhance connectivity with more extensive 30 patches of vernal pool complex and grassland habitat areas adjacent to the Plan Area. The 31 restoration and protection of vernal pool shrimp habitat is expected to provide conditions 32 favorable for maintaining and increasing the distribution and abundance of the vernal pool 33 shrimp species and their habitats. The implementation of BDCP actions to restore tidal habitat 34 will result in the permanent loss of 42 acres of vernal pool complex (see in Conservation Zones 1 35 and 11(see Table 5-4). Additionally, 5 acres of the degraded vernal pool complex vegetation 36 type will be lost but that vegetation type is ephemeral habitat that is primarily a byproduct of 37 agricultural land management actions and therefore is not considered to be the removal of vernal 38 pool shrimp species habitat. The extent of vernal pool shrimp species habitat restored and 39



protected at the near-term and early long-term evaluation points exceeds the extent that will be 1 removed by BDCP actions at those evaluation points. 2

With the full implementation of the BDCP, in the Plan Area there will be an increase in 158 3 acres of vernal pool shrimp species habitat through restoration, representing a 2 percent increase, 4 and the extent of protected existing habitat will increase by 300 acres or 11 percent (Table 5-4). 5

5.4.3.26.1 Population-Level Effects on Vernal Pool Shrimp Species 6 BDCP actions will not have either an adverse or a beneficial population-level effect on vernal 7 pool shrimp species. Although habitat restoration will increase the extent of their vernal pool 8 complex habitat by 2 percent within the Plan Area and will enhance 300 acres of existing habitat, 9 the Plan Area is located at the margin of the distribution of vernal pool shrimp species habitat 10 within the Central Valley and thus, beneficial and adverse effects of BDCP actions are unlikely 11 to affect the status of vernal pool shrimp species populations beyond the Plan Area. 12

5.4.3.26.2 Effects on Critical Habitat 13 Designated critical habitat for vernal pool tadpole shrimp, Conservancy fairy shrimp, and vernal 14 pool fairy shrimp is located in the Plan Area along the northern margin of Suisun Marsh in 15 Conservation Zone 11. The Critical Habitat includes vernal pool tadpole shrimp Unit 11D, 16 Conservancy fairy shrimp Unit 3, and vernal pool fairy shrimp Unit 16A. 17

Critical Habitat\PCEs for all three species are: 18

1) Topographic features characterized by mounds and swales, and depressions within a 19 matrix of surrounding uplands that result in complexes of continuously, or intermittently, 20 flowing surface water in the swales connecting the pools described in PCE (2), providing 21 for dispersal and promoting hydroperiods of adequate length in the pools. 22

2) Depressional features including isolated vernal pools with underlying restrictive soil 23 layers that become inundated during winter rains and that continuously hold water for a 24 minimum time period (41 days for vernal pool tadpole shrimp, 19 days for Conservancy 25 fairy shrimp, 18 days for vernal pool fairy shrimp) in all but the driest years; thereby 26 providing adequate water for incubation, maturation, and reproduction. As these features 27 are inundated on a seasonal basis, they do not promote the development of obligate 28 wetland vegetation habitats typical of permanently flooded emergent wetlands. 29

3) Sources of food, expected to be detritus occurring in the pools, contributed by overland 30 flow from the pools' watershed, or the results of biological processes within the pools 31 themselves, such as single-celled bacteria, algae, and dead organic matter, to provide for 32 feeding. 33

4) Structure within the pools described in PCE (2), consisting of organic and inorganic 34 materials, such as living and dead plants from plant species adapted to seasonally 35



inundated environments, rocks, and other inorganic debris that may be washed, blown, or 1 otherwise transported into the pools, that provide shelter. 2

The only BDCP action that could affect these Critical Habitat Units is restoration of tidal habitat 3 by restoring tidal action to areas that historically were tidal and the resulting reduced tidal prism 4 resulting from those restoration actions (see Appendix E21). PCE 1 does not exist within those 5 areas of designated critical habitat that could be affected because no vernal pool features are 6 present below the historic tide level; PCE 2 does not exist within those areas of designated 7 critical habitat that could be affected because the tidal area is inundated twice a day by tides and 8 not seasonally during winter rains; PCE 3 does not exist within those areas of designated critical 9 habitat that could be affected because these are tidal areas and not vernal pools; and PCE 4 does 10 not exist within those areas of designated critical habitat that could be affected because these 11 areas are tidal areas and not vernal pools. Consequently, tidal habitat restoration actions will 12 have no effect on any of the four PCEs and thus will not diminish the value of any affected 13 designated critical habitat for conservation of vernal pool tadpole shrimp, Conservancy fairy 14 shrimp, and vernal pool fairy shrimp. 15

5.4.3.27 Vernal Pool Plant Species (Alkali Milk-Vetch, San Joaquin Spearscale, 16 Boggs Lake Hedge-Hyssop, Heckard’s Peppergrass, Dwarf 17 Downingia, and Legenere) 18

Implementation of all BDCP actions will result in an overall benefit to the vernal pool plant 19 species through the restoration of 200 acres vernal pool complex and the protection and 20 enhancement of 300 acres of existing vernal pool complex. The restored and protected habitat 21 areas will be located such that they will maintain and enhance connectivity with more extensive 22 patches of vernal pool complex and grassland habitat areas adjacent to the Plan Area. The 23 restoration and protection of the vernal pool plant species and their habitat is expected to provide 24 conditions favorable for maintaining and increasing the distribution and abundance of vernal 25 pool plant species and their habitats within the Plan Area. The implementation of BDCP actions 26 to restore tidal habitat will result in the permanent loss of 88 acres of vernal pool complex 27 (Conservation Zones 1 and 11 (see Table 5-3). Additionally, 5 acres of affected degraded vernal 28 pool complex vegetation type will be lost but that vegetation type is ephemeral habitat that is 29 primarily a byproduct of agricultural land management actions and therefore is not considered to 30 be the removal of vernal pool plant species habitat. The extent of vernal pool plant species 31 habitat restored and protected at the near-term and early long-term evaluation points exceeds the 32 extent that will be removed by BDCP actions at those evaluation points. 33

With the full implementation of the BDCP, in the Plan Area there will be an increase of 34 112 acres of vernal pool plant species habitat through restoration, representing a 2 percent 35 increase, and the extent of protected existing habitat will increase by 300 acres or 11 percent 36 (Table 5-4). 37



5.4.3.27.1 Population-Level Effects on Vernal Pool Plant Species 1 BDCP actions will not have either an adverse or a beneficial population-level effect on vernal 2 pool plant species. Although habitat restoration will increase the extent of their vernal pool 3 complex habitat by 2 percent within the Plan Area and will enhance 300 acres of existing habitat, 4 the Plan Area is located at the margin of the distribution of their vernal pool habitats within the 5 Central Valley and thus, the beneficial and adverse effects of BDCP actions are unlikely to affect 6 the status of vernal pool plant species populations beyond the Plan Area. 7

5.4.3.28 Heartscale and Brittlescale 8

Implementation of all BDCP actions will result in an overall benefit to heartscale and brittlescale 9 through the protection and enhancement of 150 acres of existing habitat and the protection of at 10 least 3 occurrences of each species. The protected habitat areas will be located such that they 11 will maintain and enhance connectivity with more extensive patches of habitat areas adjacent to 12 the Plan Area. The protection of heartscale and brittlescale, three additional occurrences, and 13 their habitat is expected to provide conditions favorable for maintaining and increasing the 14 distribution and abundance of heartscale and brittlescale and their habitat within the Plan Area. 15 The implementation of BDCP actions to restore tidal habitat will result in the permanent loss of 16 10 acres of heartscale and brittlescale habitat (Conservation Zones 1, 8, and/or 11) (Table 5-3). 17 The extent of heartscale and brittlescale habitat restored and protected at the near-term and early 18 long-term evaluation points exceeds the extent that will be removed by BDCP actions at those 19 evaluation points. 20

With the full implementation of the BDCP, there will be a 115 percent increase in the extent of 21 existing protected habitat and 3 additional occurrences of each species will be protected 22 (Table 5-4). 23

5.4.3.28.1 Population-Level Effects on Heartscale and Brittlescale 24 BDCP actions will not have an adverse or beneficial population-level effect on either heartscale 25 or brittlescale. Although BDCP actions will protect and enhance 150 acres of heartscale or 26 brittlescale habitat and protect 3 occurrences of each species, the Plan Area is located at the 27 margin of the species distribution within the Central Valley and thus the effects of BDCP actions 28 are unlikely to affect the range-wide status of heartscale and brittlescale populations beyond the 29 Plan Area. 30

5.4.3.29 Slough Thistle 31

Implementation of all BDCP actions will result in an overall benefit to slough thistle through the 32 restoration of at least 1,000 acres of seasonally inundated floodplain habitat. The restoration of 33 seasonally inundated floodplain habitat is expected to provide conditions favorable for 34 maintaining and increasing the distribution and abundance of slough thistle within the Plan Area. 35 The implementation of BDCP actions to restore tidal habitat will result in the permanent loss of 36 5 acres of slough thistle modeled habitat, the temporary removal of 6 acres of habitat, the 37



periodic inundation of 6 acres of habitat, and the indirect disturbance of 25 acres of habitat 1 (Table 5-3). The extent of slough thistle habitat restored and protected at the near-term and early 2 long-term evaluation points exceeds the extent that will be removed by BDCP actions at those 3 evaluation points. 4

With the full implementation of the BDCP, in the Plan Area there will be an increase in the 5 extent of seasonally inundated flood plain habitat that will support patches of slough thistle 6 habitat within the Plan Area of at least 1,000 acres and there will be an increase in the extent of 7 existing protected habitat of over 532 percent (Table 5-4). 8

5.4.3.29.1 Population-Level Effects on Slough Thistle 9 BDCP actions will not have either an adverse or a beneficial population-level effect on slough 10 thistle. Although BDCP actions will restore 1,000 acres of slough thistle habitat that will create 11 the potential for increase the abundance and distribution of the species in the Plan Area, the Plan 12 Area is located much further north than slough thistle’s population center which exists in the 13 areas of former lake beds in the southern San Joaquin Valley. 14

5.4.3.30 Suisun Thistle and Soft Bird’s-beak 15

Implementation of all BDCP actions will result in an overall benefit to slough thistle through the 16 restoration of between 3,600 and 4,800 acres of tidal brackish marsh habitat (based on the RMA 17 hypothetical tidal habitat restorations described in Appendix N.3, RMA Description of 18 Hypothetical Restoration Design and Effects) which will contain areas of suitable habitat for 19 these species and the protection of at least 3 occurrences of each species. The restoration of tidal 20 brackish marsh habitat is expected to provide conditions favorable for maintaining and 21 increasing the distribution and abundance of Suisun thistle and soft bird’s-beak within the Plan 22 Area. The implementation of BDCP actions to restore tidal habitat will result in the permanent 23 loss of 636 acres of Suisun thistle and soft bird’s-beak habitat (Table 5-3). The extent of Suisun 24 thistle and soft bird’s-beak habitat restored at the near-term and early long-term evaluation points 25 exceeds the extent that will be removed by BDCP actions at those evaluation points. 26

With the full implementation of the BDCP, in the Plan Area the extent of protected tidal brackish 27 marsh that could support areas of Suisun thistle and soft bird’s-beak habitat within the Plan Area 28 will be increased between 347 and 485 percent and 3 additional occurrences of each species will 29 be protected (Table 5-4). 30

5.4.3.30.1 Population-Level Effects on Suisun Thistle and Soft Bird’s-beak 31

BDCP actions will have beneficial population-level effects on Suisun thistle and soft bird’s-beak. 32 BDCP actions will restore between 3,600 and 4,800 acres of tidal brackish wetland habitat and 33 protect 3 occurrences of each species. Suisun thistle is endemic to the Plan Area and Suisun 34 Marsh represents a large portion of soft bird’s-beak overall population. Thus, beneficial effects 35 of BDCP actions could affect the range-wide status of Suisun thistle and soft bird’s-beak 36 populations. 37



5.4.3.30.2 Effects on Critical Habitat 1 Designated critical habitat for the Suisun thistle and soft bird’s-beak is located in the Plan Area 2 exclusively in tidal areas of Suisun Marsh. Suisun thistle Unit 1 and soft bird’s-beak Unit 2 are 3 located at Hill Slough Marsh, Suisun thistle Unit 2 is located at Petonia Slough Marsh, Suisun 4 thistle Unit 3 and soft bird’s-beak Unit 4 are located at Rush Ranch/Grizzly Island Wildlife Area. 5

Critical Habitat PCEs for Cirsium hydrophilum var. hydrophilum are: 6

1) Persistent emergent, intertidal, estuarine wetland at or above the mean high-water line (as 7 extended directly across any intersecting channels); 8

2) Open channels that periodically contain moving water with ocean-derived salts in excess 9 of 0.5 percent; and 10

3) Gaps in surrounding vegetation to allow for seed germination and growth. 11

Critical Habitat PCEs for Cordylanthus mollis ssp. mollis are: 12

1) Persistent emergent, intertidal, estuarine wetland at or above the mean high-water line (as 13 extended directly across any intersecting channels); 14

2) Rarity or absence of plants that naturally die in late spring (winter annuals); and 15

3) Partially open spring canopy cover (approximately 790 nanomoles per square meter per 16 second [nMol/m2/s]) at ground level, with many small openings to facilitate seedling 17 germination. 18

As modeled in the hypothetical tidal habitat restorations (see Appendix N.3, RMA Description of 19 Hypothetical Restoration Design and Effects), tidal habitat restoration actions under full 20 implementation of the BDCP will alter the tidal prism and will result in the compression of the 21 tidal range by approximately 1 foot biased towards a lower elevation of mean lower low water. 22 The result will be the loss of an undeterminable amount of designated critical habitat due to a 23 lowered mean high-water line (PCE1 for both species). 24

The potential for effects on designated critical habitat will be minimized through design of tidal 25 habitat restoration projects and temporal and spatial staging of when and where restoration 26 projects are implemented. Implementation of the tidal habitat restoration projects are expected to 27 restore patches of Suisun thistle and soft bird’s-beak habitat and to contribute to the achieving 28 the objectives of the Draft Recovery Plan for Tidal Marsh Ecosystems of Northern and Central 29 California (USFWS 2010). Consequently, any adverse effects of habitat restoration on 30 designated critical habitat are not expected to appreciably diminish the value of critical habitat 31 for species conservation. 32



5.4.3.31 Delta Button Celery 1

Implementation of all BDCP actions will result in an overall benefit to Delta button celery 2 through the protection of at least 100 acres of alkali habitat and the restoration of at least 1,000 3 acres of seasonally inundated floodplain habitat that will support areas of Delta button celery 4 habitat. The restoration and protection of Delta button celery habitat is expected to provide 5 conditions favorable for maintaining and increasing the distribution and abundance of Delta 6 button celery and its habitat within the Plan Area. The implementation of BDCP actions to 7 restore tidal habitat will result in the permanent loss of 25 acres of Delta button celery habitat, 8 the temporary removal of 8 acres of habitat, the periodic inundation of 18 acres of habitat 9 (Table 5-3). The extent of Delta button celery habitat restored and protected at the near-term and 10 early long-term evaluation points exceeds the extent that will be removed by BDCP actions at 11 those evaluation points. 12

With the full implementation of the BDCP, there will be a 407 percent increase in the extent of 13 existing protected habitat (Table 5-4). 14

5.4.3.31.1 Population-Level Effects on Delta Button Celery 15 BDCP actions will not have either an adverse or a beneficial population-level effect on Delta 16 button celery. Although BDCP actions will protect at least 100 acres of existing habitat and 17 restore at least 1,000 acres of Delta button celery habitat that will create the potential for 18 increasing the abundance and distribution of the species in the Plan Area, the Plan Area is 19 located at the northern edge of its range and thus will be unlikely to have a population-level 20 effect on the species’ abundance and distribution. 21

5.4.3.32 Inland Dune Scrub Plant Species (Contra Costa Wallflower, Antioch 22 Dunes Primrose) 23

Implementation of the BDCP will result in overall beneficial effects on Contra Costa wallflower 24 and Antioch Dunes primrose. BDCP actions will have no adverse effect on Contra Costa 25 wallflower and Antioch Dunes primrose or their habitat. BDCP support for USFWS habitat 26 enhancement and propagation programs are expected to maintain and potentially increase the 27 abundance of Contra Costa wallflower and Antioch Dunes primrose. 28

5.4.3.32.1 Population-Level Effects on Inland Dune Scrub Plant Species 29 BDCP support of USFWS restoration and enhancement actions at the Antioch Dunes NWR will 30 have beneficial population-level effects on Contra Costa wallflower and Antioch Dunes 31 primrose. BDCP support will help restore inland dune scrub habitat and augment existing 32 populations throughout-planting of nursery grown stock into areas of inland dune scrub plant 33 habitat. Both Contra Costa wallflower and Antioch Dunes evening primrose are subspecies that 34 are endemic to the Plan Area. Thus, beneficial effects of BDCP actions could affect the range-35 wide status of Contra Costa wallflower and Antioch Dunes evening primrose. 36



5.4.3.32.2 Effects on Critical Habitat 1 Designated critical habitat for Contra Costa wallflower and Antioch Dunes primrose is located in 2 the Plan Area on the Antioch Dunes NWR refuge and slightly into the San Joaquin River. It is 3 designated as “an area of land, water, and airspace (exclusive of those existing man-made 4 structures or settlements which are not necessary to the survival or recovery of the species) in 5 Contra Costa County.” Inland dune scrub actions supported by the BDCP will be implemented 6 by the USFWS and will have no adverse effect on the designated critical habitat. Any habitat 7 enhancement actions for these species in designated critical habitat are expected to enhance and 8 not diminish the value of any affected designated critical habitat for conservation of Contra 9 Costa wallflower and Antioch Dunes primrose. Proposed changes in water operations will 10 periodically alter the salinity or temperature of the water but will not affect the sediment supply 11 to the due so will have no adverse effect on the designated critical habitat. 12

5.4.3.33 Carquinez Goldenbush 13

Implementation of all BDCP actions will result in an overall benefit to Carquinez goldenbush 14 through the protection and enhancement of 300 acres of existing habitat and the protection of at 15 least 3 occurrences. The protected habitat areas will be located such that they will maintain and 16 enhance connectivity with more extensive patches of habitat areas adjacent to the Plan Area. The 17 protection of Carquinez goldenbush, its occurrences, and its habitat is expected to provide 18 conditions favorable for maintaining and increasing the distribution and abundance of Carquinez 19 goldenbush and its habitats within the Plan Area. The implementation of BDCP actions to restore 20 tidal habitat will result in the permanent loss of 42 acres of Carquinez goldenbush habitat and 21 temporarily disturb 17 acres of Carquinez goldenbush habitat (Table 5-3). The extent of 22 Carquinez goldenbush habitat restored and protected at the near-term and early long-term 23 evaluation points exceeds the extent that will be removed by BDCP actions at those evaluation 24 points. 25

With the full implementation of the BDCP, there will be a 76 percent increase in the extent of 26 existing protected habitat and 3 additional occurrences of Carquinez goldenbush will be 27 protected (Table 5-4). 28

5.4.3.33.1 Population-Level Effects on Carquinez Goldenbush 29

BDCP actions will have a beneficial population-level effect on Carquinez goldenbush. The 30 species’ range is limited to Solano County, a large portion of which is located in the Plan Area. 31 Implementation of the BDCP will increase the extent of protected and managed Carquinez 32 goldenbush habitat from 38 percent to 70 percent within the Plan Area and protect all remaining 33 known occurrences in the Plan Area. 34

5.4.3.34 Delta Tule Pea and Suisun Marsh Aster 35

Implementation of all BDCP actions will result in an overall benefit to Delta tule pea and Suisun 36 Marsh aster through the restoration of between 16,970 to 26,470 acres of tidal marsh habitat 37



(based on the RMA hypothetical tidal habitat restorations described in Appendix N.3, RMA 1 Description of Hypothetical Restoration Design and Effects) which will contain areas of suitable 2 habitat for these species. The restoration of Delta tule pea and Suisun Marsh aster habitat is 3 expected to provide conditions favorable for maintaining and increasing the distribution and 4 abundance of Delta tule pea and Suisun Marsh aster and their habitat within the Plan Area. The 5 implementation of BDCP actions to restore tidal habitat will result in the permanent loss of 6 1,137 acres, the temporary disturbance of 1 acre, and the periodic inundation of 10 acres of Delta 7 tule pea and Suisun Marsh aster habitat (Table 5-3). The extent of Delta tule pea and Suisun 8 Marsh aster habitat restored and protected at the near-term and early long-term evaluation points 9 exceeds the extent that will be removed by BDCP actions at those evaluation points. 10

With the full implementation of the BDCP, there will be an increase in the extent of tidal habitat 11 with areas of Delta tule pea and Suisun Marsh aster habitat within the Plan Area by 16,970 to 12 26,470 acres and there will be an increase in the extent of existing protected tidal habitat with 13 areas of Delta tule pea and Suisun Marsh aster habitat of between 430 and 687 percent 14 (Table 5-4). 15

5.4.3.34.1 Population-Level Effects on Delta Tule Pea and Suisun Marsh Aster 16 BDCP actions will have beneficial population-level effects on Delta tule pea and Suisun Marsh 17 aster. BDCP actions will restore 16,970 to 26,470 acres of tidal wetland habitat. Delta tule pea 18 and Suisun Marsh aster are nearly endemic to the Plan Area. Thus, beneficial effects of BDCP 19 actions could beneficially affect the range-wide status of Delta tule pea and Suisun Marsh aster. 20

5.4.3.35 Delta Mudwort and Mason’s Lilaeopsis 21

Implementation of all BDCP actions will result in an overall benefit to Delta mudwort and 22 Mason’s lilaeopsis through the restoration of between 16,980 to 26,560 acres of tidal marsh 23 habitat (based on the RMA hypothetical tidal habitat restorations described in Appendix N3, 24 RMA Description of Hypothetical Restoration Design and Effects) which will contain areas of 25 suitable habitat for these species. The restoration of Delta mudwort and Mason’s lilaeopsis 26 habitat is expected to provide conditions favorable for maintaining and increasing the 27 distribution and abundance of Delta mudwort and Mason’s lilaeopsis and their habitat within the 28 Plan Area. The implementation of BDCP actions to restore tidal habitat will result in the 29 permanent loss of 146 acres, the temporary disturbance of 9 acres, and the periodic inundation of 30 205 acres of Delta mudwort and Mason’s lilaeopsis habitat (Table 5-3). The extent of Delta 31 mudwort and Mason’s lilaeopsis habitat restored and protected at the near-term and early long-32 term evaluation points exceeds the extent that will be removed by BDCP actions at those 33 evaluation points. 34

With the full implementation of the BDCP, there will be an increase in the extent of tidal habitat 35 with areas of Delta mudwort and Mason’s lilaeopsis habitat within the Plan Area by 16,980 to 36 26,560 acres and there will be an increase in the extent of existing protected tidal habitat with 37



areas of Delta mudwort and Mason’s lilaeopsis habitat of between 984 and 1,542 percent 1 (Table 5-4). 2

5.4.3.35.1 Population-Level Effects on Delta Mudwort and Mason’s Lilaeopsis 3 BDCP actions will have beneficial population-level effects on Delta mudwort and Mason’s 4 lilaeopsis. BDCP actions will restore 16,980 to 26,560 acres of tidal wetland habitat that will 5 contain areas of delta mudwort and Mason’s lilaeopsis habitat. Delta mudwort and Mason’s 6 lilaeopsis are nearly endemic to the Plan Area. Thus, beneficial effects of BDCP actions could 7 affect the range-wide status of Delta mudwort and Mason’s lilaeopsis. 8

5.4.3.36 Side-flowering Skullcap 9

Implementation of all BDCP actions will result in an overall benefit to side-flowering skullcap 10 through the restoration of 5,000 acres of valley/foothill riparian community and between 13,900 11 and 21,600 acres of tidal freshwater emergent wetland community (based on the RMA 12 hypothetical tidal habitat restorations described in Appendix N.3, RMA Description of 13 Hypothetical Restoration Design and Effects). The restoration of the two communities is 14 expected to provide conditions favorable for maintaining and increasing the distribution and 15 abundance of side-flowering skullcap and its habitat within the Plan Area. The implementation 16 of BDCP actions to restore tidal habitat will result in the permanent loss of 37 acres, temporarily 17 disturb 3 acres, and periodically inundate 41 acres of side-flowering skullcap habitat (Table 5-3). 18 The extent of side-flowering skullcap habitat restored and protected at the near-term and early 19 long-term evaluation points exceeds the extent that will be removed by BDCP actions at those 20 evaluation points. 21

Because of its unique habitat, decaying stumps and pilings, with the full implementation of the 22 BDCP there will be an indeterminable increase in the extent of existing protected habitat of side-23 flowering skullcap. 24

5.4.3.36.1 Population-Level Effects on Side-flowering Skullcap 25 BDCP actions will have beneficial population-level effects on side-flowering skullcap. BDCP 26 actions will restore 5,000 acres of valley/foothill riparian community and between 13,900 and 27 21,600 acres of tidal freshwater emergent wetland community containing patches of side-28 flowering skullcap habitat. Within California, side-flowering skullcap is endemic to the Plan 29 Area while it is widely distributed across the United States and Canada. Thus, beneficial effects 30 of BDCP actions will not affect the range-wide status of side-flowering skullcap. 31

5.4.3.37 Caper-fruited Tropidocarpum 32

Implementation of all BDCP actions will result in an overall benefit for caper-fruited 33 tropidocarpum within the Plan Area by protecting and enhancing at least 100 acres of its 34 modeled habitat to provide conditions favorable for reestablishing caper-fruited tropidocarpum in 35 the Plan Area. Any occurrences that establish on protected BDCP lands will be managed to 36



maintain and increase the extent of occupied habitat and the abundance of caper-fruited 1 tropidocarpum plants. Adverse effects on caper-fruited tropidocarpum from implementing 2 BDCP includes the temporary removal of 34 acres caper-fruited tropidocarpum habitat through 3 deposits of spoils generated during conveyance construction activities (Table 5-3). Full 4 implementation of BDCP will result in protection of 9 percent of caper-fruited tropidocarpum 5 within the Plan Area, and increase of 476 percent in the extent of protected habitat (Table 5-4). 6

5.4.3.37.1 Population-Level Effects on Caper-fruited Tropidocarpum 7 BDCP actions are expected to have no adverse population-level effect on caper-fruited 8 tropidocarpum and could have a beneficial population-level effect if one or more occurrences of 9 this species, which is believed to be extirpated from the Plan Area, become established. BDCP 10 direct effects on caper-fruited tropidocarpum are limited to 34 acres of modeled caper-fruited 11 tropidocarpum habitat which will be temporarily removed through deposits of spoils generated 12 during conveyance construction activities. This will result in no or very little effect on the 13 species’ total distribution.14



Table 5-1. Summary of Impacts on the Extent of Natural Communities with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point)

Natural Community

A B C D=(A-B)+C [(D-A)/A]-1*100

Existing Extent (acres)

Permanently Removed (acres)1

Temporarily Removed (acres) 2

Periodically Removed (acres) 3 Restored (acres)

Future Extent with Full BDCP Implementation

(acres) Percent Change

in Extent Tidal perennial aquatic 4 86,240 46 69 39 25,000-32,0005 111,194 – 118,194 29-37Tidal mudflat6 Not available Not available Not available Not available Not available Not available Not availableTidal brackish emergent wetland 7 8,351 515 0 0 3,600-4,800 5 11,436 – 12,636 37-51Tidal freshwater emergent wetland 7 8,947 41 4 231 13,200 – 21,600 5 21,106-30,506 136-241Valley foothill riparian 17,338 1,114 165 589 5,000 21,223 22Grassland 62,880 2,831 437 2,111 2,000 62,049 -1Alkali seasonal wetland complex 3,722 136 0 825 0 3,586 -4Vernal pool complex 6,959 88 0 0 200 7,071 2Other natural seasonal wetland 264 1 0 2 0 263 0Non-tidal permanent freshwater emergent wetland 9 1,134 92 0 8 200 1,242 10Non-tidal perennial aquatic 9 5,341 245 37 329 200 5,295 -1Managed wetlands 64,844 12,196 48 2,477 0 52,648 -19Inland Dune Scrub 19 0 0 0 0 19 0Agricultural lands 10 Alfalfa 82,282 10,398 541 2,277 0 71,884 -13 Irrigated Pasture 49,694 3,692 44 1,409 0 46,002 -7 Vineyard 28,901 1,844 470 336 0 27,058 -6 Orchard 18,019 498 321 85 0 17,520 -3 Rice 12,637 0 0 4,585 0 12,637 0 Other Cultivated Crops 229,828 18,900 2,152 9,532 0 210,928 -8 Subtotal: Cropland only 421,361 35,333 3,527 18,223 0 386,028 -8 Other Agricultural lands 82,418 6,283 500 2,619 0 76,135 -8 Subtotal: All agricultural land 503,779 41,615 4,027 20,842 0 462,163 -8Notes: 1. Permanent impacts represent those associated with construction of forebays, Intake facilities, permanent access roads, shaft locations, muck areas, levee setback footprints, riparian

restoration areas, nontidal marsh restoration and conservation hatcheries facilities. 2. Features in this category include the following conveyance features: Barge Unloading Facility, Control Structure Work Area, Intake Road Work Area, Intake Work Area, Pipeline,

Pipeline Work Area, Road Work, Borrow and Spoils sites, Area, Safe Haven Work Area, Temporary Access Road Work Area, Tunnel Work Area. 3. Periodic impacts represent those associated with the periodic flooding of the Yolo Bypass and floodplain setbacks along the San Joaquin River. 4. Tidal Perennial Aquatic impacts related to the intake right of ways have been removed as it is assumed that these would not pose an impact to this natural community. Tidal restoration

impacts were assessed based on areas expected to become desiccated based on RMA modeling results. 5. As modeled in the hypothetical tidal habitat restorations, see Appendix Z [RMA tech #4 & SAIC memo]). 6. Tidal mudflat features were not mapped within the BDCP vegetation layer, however will be evaluated in linear miles of tidal marsh/shallow subtidal aquatic interface. 7. Impacts assessed for tidal marsh restoration reflect those incurred to tidal brackish emergent wetland habitat components expected to be desiccated based on RMA modeling results. 8. Actual sum of 400 acres may be distributed differently between non-tidal perennial aquatic and non-tidal permanent freshwater emergent wetland communities. 9. Does not include removal of agricultural lands to restore 2,000 acres of grassland and 200 acres of vernal pools. These effects will be included in the next version of this table.



Table 5-2. Summary of Conservation Provided for Natural Communities with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point)

Natural Community

Existing Extent (acres) Permanently Removed (acres)1 [E=A-C] Extent

Remaining

[F=B-D] Remaining Existing

Protected Habitat

[G] Protected Under BDCP

(acres)

[H] Restored Under BDCP (acres)

[I=G+H] Total Conserved

Under BDCP (acres)

Total Protected with Full BDCP Implementation [L=( J-B)/B]

Percent Change in Extent of Protected from Extent of

Existing Protected [A] Total [B] Extent Protected [C] Total

[D] Permanently Removed Protected

[J=F+I] [K=J/(E+H)]*100Percent Protected

Tidal perennial aquatic 2 86,240 18,080 46 30 86,194 18,050 0 1 25,000-32,000 2 25,000-32,000 1,2 43,050-50,050 1,2 38.7 to 42.3 138-177

Tidal mudflat3 Not

available Not

available Not

available Not available Not available Not available 0 1 Not available4 Not available4 Not available4 Not available4 Not available4

Tidal brackish emergent wetland 4 8,351 5,102 515 485 7,836 4,616 0 1 3,600-4,800 2 3,600-4,800 1,2 8,216-9,416 1,2 71.8 to 74.5 61-85

Tidal freshwater emergent wetland 4 8,947 4,990 41 17 8,905 4,973 0 1 13,200-21,600 2 13,200-21,600 1,2 18,173-26,573 1,2 82.2 to 87.1% 264-433

Valley foothill riparian 17,338 5,338 1,114 730 16,223 4,608 0 1 5,000 5,000 1 9,608 1 45.30 80 Grassland 62,880 14,984 2,831 1,010 60,049 13,974 8,0001 2,000 10,000 1 23,974 1 38.60 60 Alkali seasonal wetland complex 3,722 2,769 136 57 3,586 2,712 400 0 400 3,112 86.80 12

Vernal pool complex 6,959 4,379 88 30 6,871 4,349 300 200 500 4,849 68.60 11 Other natural seasonal wetland 264 205 1 0 263 205 0 1 0 0 1 205 1 78 0 Non-tidal permanent freshwater emergent wetland 5 1,134 408 92 48 1,042 360 0 1 200 200 1 560 1 45.1 37.3

Non-tidal perennial aquatic 5 5,341 1,239 245 51 5,095 1,188 0 1 200 200 1 1,388 1 26.20 12.0 Managed wetlands 64,844 52,676 12,196 10,649 52,648 42,027 0 6 0 6 0 6 42,0276 79.8 6 -20.20 Inland Dune Scrub 19 17 0 0 19 17 0 0 0 17 90 0 Agricultural lands 6 Alfalfa 82,282 3,665 10,398 374 71,884 3,291 Not available6 0 Not available6 Not available6 Not available6 Not available6 Irrigated Pasture 49,694 12,748 3,692 1,240 46,002 11,508 Not available5 0 Not available6 Not available6 Not available6 Not available6 Vineyard 28,901 2,476 1,844 210 27,058 2,266 0 0 0 2,266 8.4 -8 Orchard 18,019 343 498 66 17,520 277 0 0 0 278 1.6 -19 Rice 12,637 2,202 0 0 12,637 2,202 4,600 0 4,600 6,802 53.8 209 Other Cultivated Crops 229,828 24,736 18,900 2,924 210,928 21,812 Not available5 0 Not available6 Not available6 Not available6 Not available6 Subtotal: Cropland only 421,361 46,171 35,333 4,814 386,028 41,357 16,620-32,640 0 16,620-32,640 57,976-73,996 15 to 19.2 26-60 Other Agricultural lands 82,418 10,997 6,283 1,746 76,135 9,251 0 0 0 9,252 12.2 -16 Subtotal: All agricultural land 503,779 57,168 41,615 6,560 462,163 50,608 16,620-32,640 0 16,620-32,640 67,228-83,248 14.6 to 18.0 18-46

Total 769,818 167,338 58,922 19,668 710,896 147,671 25,320-41,3407 50,113-65,692 75,433-107,032 223,104-254,703 29.3% to 32.8% 33-52

Notes: 1. Includes both non-tidal freshwater permanent emergent wetland and non-tidal perennial aquatic and does not include patches of these communities that are present on BDCP lands acquired for other purposes and that would be incidentally protected under

BDCP.2Based on RMA modeling of hypothetical tidal habitat restoration footprints. 3. The extent of existing tidal mudflat cannot be delineated based on available information. 4. The extent of total tidal mudflat that will develop as a component of 65,000 acres of tidal habitat restoration could not be reasonably predicted with the models developed. BDCP biological objectives, however, require establishment of at least 20 linear

miles of tidal mudflat substrate. 5. Actual sum of 400 acres may be distributed differently between non-tidal perennial aquatic and non-tidal permanent freshwater emergent wetland communities 6. The mix of alfalfa, irrigated pasture, and other cultivated crops annually maintained under the BDCP will vary among years over the term of the BDCP depending on market drivers on growers with conservation easements. 7. Does not include acquisition of any additional lands associated with restoration of 65,000 acres of tidal habitat that may be required to provide transitional upland and sea level rise accommodation space.



Table 5-3. Summary of Impacts on the Extent of Covered Wildlife and Plant Species Habitats with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point)

Covered Species

A B Temporarily

Removed (acres)2

Periodically Removed (acres)

C D=(A-B)+C [(D-A)/A]*100


Permanently Removed (acres) 1

Restored (acres)


(acres)

Percent Change in

Extent

Mammals San Joaquin kit fox

Breeding, Foraging, and Dispersal Habitat 5,217 163 161 0 0 5,054 -3.1

Foraging and Dispersal Habitat 20,573 663 481 0 0 19,911 -3.2 Total 25,791 826 642 0 0 24,965 -3.2 Riparian woodrat

Habitat 1,539 25 14 98 300 1,814 17.9 Salt marsh harvest mouse

Wetland habitat 11,124 2,487 0 0 3,600-4,800 3 12,237 - 13,437 10.0 to 20.8 Upland habitat 2,815 674 0 0 350-700 2,491 - 2,841 -11.5 to 1.0

Total 13,940 3,161 0 0 3,950-5,500 3 14,729 -16,279 5.7 to 16.8 Riparian brush rabbit

Habitat 2,894 62 19 264 300 3,132 8.2 Townsend’s big-eared bat

Primary foraging habitat 10,880 860 76 291 0 10,020 -7.9 Roosting and primary foraging habitat 6,892 268 86 301 5,000 11,624 68.7 Secondary foraging habitat 753,408 60,051 4,592 30,619 0 693,357 -8.0

Total 771,180 61,179 4,754 31,211 5,000 715,001 -7.3 Suisun shrew

Habitat 28,742 6,237 0 0 3,600-4,800 3 26,105 - 27,305 -9.2 to -5.0 Birds Tricolored blackbird

Nesting habitat 24,036 4,104 35 303 17,900-26,800 37,832 - 46,732 57.4 to 94.4 Foraging habitat: non agriculture 99,587 5,878 471 5,414 0 93,709 -5.9 Foraging habitat: agriculture 275,937 24,781 1,959 6,599 0 251,156 -9.0

Total 399,560 34,763 2,465 12,316 17,900-26,800 382,697 - 391,597 -4.2 to -2.0 Suisun song sparrow

Habitat 26,958 5,272 0 0 3,600-4,800 3 25,286 -26,486 -6.2 to -1.8



Table 5-4. Summary of Impacts on the Extent of Covered Wildlife and Plant Species Habitats with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point) (continued)

Covered Species

A B Temporarily

Removed (acres)2


C D=(A-B)+C [(D-A)/A]*100



Restored (acres)


(acres)

Percent Change in

Extent

Yellow-breasted chat Primary Nesting and Migratory Habitat 7,384 351 22 203 >2,000 7,233 -2.0 Secondary Nesting and Migratory Habitat 5,530 468 12 94 <3,000 5,362 -3.0

Suisun Marsh/Upper Yolo Bypass Nest and Migratory Habitat 1,256 230 95 145 0 1,026 -18.3

Total 14,171 1,049 129 442 5,000 18,122 27.9 Least Bell's Vireo

Habitat 14,137 1,049 129 442 >2,000 15,088 6.7 Western burrowing owl

High-value habitat 78,447 3,569 410 2,923 2,000 76,878 -2.0 Moderate-value habitat 52,800 4,260 46 1,651 0 48,540 -8.1 Low-value habitat 243,129 21,631 1,971 10,265 0 221,498 -8.9

Total 374,377 29,460 2,427 14,839 0 344,917 -7.9 Western Yellow-billed Cuckoo

Breeding Habitat 6,825 574 112 223 >1,000 7,251 6.2 Migratory Habitat 4,890 228 12 198 0 4,662 -4.7

Total 11,715 802 124 421 >1,000 11,913 1.7 California Least Tern 2

Habitat 86,242 46 64 39 25,000 – 32,000 3 96,196 - 106,196 11.5 to 23.1 Greater sandhill crane

Roosting/Foraging Habitat 11,829 0 16 0 320 12,149 2.7 Foraging Habitat 184,257 6,739 1,318 0 0 177,518 -3.7

Total 196,086 6,739 1,334 0 320 189,667 -3.3 California black rail

Habitat 33,563 5,949 4 247 17,500-26,400 8 45,114 - 54,014 34.4 to 60.9 California clapper rail

Habitat 7,895 327 0 0 3,600-4,800 3 11,168 - 12,368 41.5 to 56.7 Swainson’s hawk

Foraging habitat 436,417 37,552 3,081 17,355 0 398,865 -8.6 Nesting habitat 10,149 706 138 440 4,000 13,443 32.5

Total 446,566 38,258 3,219 17,795 4,000 412,308 -7.7




Covered Species

A B Temporarily

Removed (acres)2


C D=(A-B)+C [(D-A)/A]*100



Restored (acres)


(acres)

Percent Change in

Extent

White-tailed kite Breeding habitat 13,714 868 145 515 4,000 16,846 22.8 Foraging habitat 478,251 44,417 3,101 20,436 0 433,834 -9.3

Total 491,965 45,285 3,246 20,951 4,000 450,680 -8.4 Reptiles Giant Garter Snake

Aquatic Breeding, Foraging and Movement 19,824 565 52 4,932 13,690-22,040 32,949 - 41,299 66.2 to 108.3

Upland Aestivation and Movement 190,805 13,713 941 5,534 0 177,092 -7.2 Total 210,629 14,278 993 10,465 13,690-22,040 210,041 - 218,391

Aquatic Breeding, Foraging and Movement (miles) 6,000 342 25 66 0 5,658 -5.7

Western pond turtle Aquatic habitat 4 78,511 6,013 84 4,046 27,900-46,800 100,398-131,324 27.9 to 67.3 Dispersal habitat 579,334 47,471 4,159 20,912 0 531,863 -8.2 Upland nesting and overwintering 54,880 4,317 363 4,163 5,000 55,563 1.2

Total 712,725 57,801 4,606 29,122 32,900-51,800 687,824-718,750 -3.5 to 0.8 Amphibians California red-legged frog

Aquatic habitat 117 1 0 0 0 117 -0.8 Upland cover and dispersal habitat 4,984 168 161 0 0 4,816 -3.4 Dispersal habitat 19,572 663 481 0 0 18,909 -3.4

Total 24,673 832 643 0 0 23,841 -3.4 Western spadefoot toad

Aquatic Breeding Habitat 6,790 48 0 0 200 6,942 2.2 Terrestrial Cover and Aestivation Habitat 14,353 464 169 0 500 14,389 0.3

Total 21,143 512 169 0 700 21,331 0.9




Covered Species

A B Temporarily

Removed (acres)2


C D=(A-B)+C [(D-A)/A]*100



Restored (acres)


(acres)

Percent Change in

Extent

California tiger salamander Aquatic breeding habitat 6,772 42 0 0 200 6,930 2.3 Terrestrial Cover and Aestivation Habitat 14,353 464 169 0 500 14,389 0.3

Total 21,125 506 169 0 700 21,319 0.9 Invertebrates Valley elderberry longhorn beetle

Riparian vegetation 17,130 1,102 150 564 5,000 21,028 22.8 Non-riparian channels and grasslands 16,022 620 202 722 0 15,402 -3.9

Total 33,152 1,722 352 1,286 5,000 36,430 9.9 Lange's metalmark butterfly

Habitat 1,108 0 0 0 0 1,108 0.0 Vernal pool tadpole shrimp

Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Conservancy fairy shrimp Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Longhorn fairy shrimp Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Vernal pool fairy shrimp Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Mid Valley fairy shrimp Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

California linderiella 0 Vernal Pool Complex 6,821 42 0 0 200 6,979 2.3 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2




Covered Species

A B Temporarily

Removed (acres)2


C D=(A-B)+C [(D-A)/A]*100



Restored (acres)


(acres)

Percent Change in

Extent

Plants Alkali milk-vetch

Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Heartscale Habitat 495 10 0 0 0 485 -2.1

Brittlescale Habitat 495 10 0 0 0 485 -2.0

San Joaquin spearscale Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Slough thistle Habitat 1,831 5 6 6 > 1,000 2,826 54.3

Suisun thistle4 Habitat 1,129 636 0 0 3,600-4,8003 4,093 - 5,293 262.5 to 368.8

Soft bird’s-beak4 Habitat 1,224 636 0 0 3,600-4,8003 4,188 - 5,388 242.2 to 340.2

Dwarf Downingia Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Delta button celery Habitat 3,344 25 8 18 > 1,000 4,319 129.2

Boggs Lake hedge-hyssop Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Carquinez goldenbush Habitat 1,032 42 0 0 0 990 -4.1

Delta tule pea Habitat 5,948 1,137 1 10 16,970-26,4703 21,781 - 31,281 266.2 to 426.0




Covered Species

A B Temporarily

Removed (acres)2


C D=(A-B)+C [(D-A)/A]*100



Restored (acres)


(acres)

Percent Change in

Extent

Legenere Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Heckard’s peppergrass Vernal pool Complex 6,959 88 0 0 200 7,070 1.6 Degraded Vernal Pool Complex 2,493 5 0 0 0 2,488 -0.2

Mason’s lilaeopsis Habitat 6,931 146 9 205 16,980-26,5603 23,765 - 33,345 242.9 - 381.1

Delta mudwort Habitat 6,931 146 9 205 16,980-26,5603 23,765 - 33,345 242.9 - 381.1

Suisun Marsh aster Habitat 5,948 1,137 1 10 16,970-26,4703 21,781 - 31,281 266.2 - 426.0

Side-flowering skullcap Habitat 2,495 37 3 41 0 2,458 -1.5

Caper-fruited tropidocarpum Habitat 1,345 0 34 0 0 1,345 0.0

Contra Costa wallflower Habitat 19 0 0 0 0 19 0.0

Antioch Dunes evening primrose Habitat 19 0 0 0 0 19 0.0

Notes: 1. Permanent impacts represent those associated with construction of forebays, Intake facilities, permanent access roads, shaft locations, muck areas, levee setback footprints,

riparian restoration areas, nontidal marsh restoration and conservation hatcheries facilities 2. Tidal perennial aquatic impacts related to the intake right of ways have been removed as it is assumed that these would not pose an impact to this natural community. Tidal

restoration impacts were assessed based on areas expected to become desiccated based on RMA modeling results. 3. As modeled in the hypothetical tidal habitat restorations, see Appendix N3 (RMA Description of Hypothetical Restoration Design and Effects).4Impacts assessed for tidal

marsh restoration reflect those incurred to habitat that are expected to experience inundation and desiccation. 1



Table 5-9. Summary of Conservation Provided for Covered Wildlife and Plant Species with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point)

Covered Species


Permanently Removed (acres) 2 [E = A-

C] Extent Remaining

[F = B-D]

Remaining

Existing

Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total

Conserved Under BDCP (acres)

Total Protected with Full BDCP

Implementation

[L=(J-B)/B] Percent

Change in Extent of Protected

from Extent of Existing Protected

[A] Total

[B] Extent Protect

ed

[C] Total

[D] Permanen

tly Removed Protected

[J=F+I] Protected

[K=(J/(E+H)]

Percent Protecte

d

Mammals San Joaquin kit fox

Breeding, Foraging, and Dispersal Habitat 5,217 638 163 81 5,054 557 1,000 8 0 1,000 8 1,557 8 30.8 144%

Foraging and Dispersal Habitat 20,573 151 663 13 19,911 138 0 8 0 0 8 138 8 1 -9%

Total 25,791 789 826 94 24,965 695 1,000 0 1,000 1,695 6.7 115% Riparian woodrat

Habitat 1,539 97 25 3 1,514 94 0 300 300 394 21.7 306% Salt marsh harvest mouse

Wetland habitat 11,124 9,600 2,487 2,369 8,637 7,231 0 8 3,600-4,800 9

3,600-4,800 9

10,831-12,031 8,9

88.5 - 89.5 13-25%

Upland habitat 2,815 2,334 674 618 2,141 1,716 350-700 8 350-700 700-1,400 8 2,415-3,115 8

96.9 -109.6 4-33%

Total 13,940 11,934 3,161 2,987 10,779 8,947 350-700 3,950-5,500 9

4,300-6,200 9

13,246-15,146 9 89.9 - 93 11-27%

Riparian brush rabbit Habitat 2,894 138 62 3 2,832 135 0 8 300 300 8 435 8 13.9 215%

Townsend’s big-eared bat Primary foraging habitat 10,880 3,641 860 582 10,020 3,059 0 8 0 0 8 3,059 8 30.5 -16% Roosting and primary

foraging habitat 6,892 1,876 268 156 6,624 1,720 0 8 5,000 5,000 8 6,720 8 57.8 258%

Secondary foraging habitat 753,408 162,668 60,051 20,467 693,35

7 142,20

1 0 8 0 0 8 142,201 8 20.5 -13%

Total 771,180 168,185 61,179 21,205 710,001

146,980 0 5,000 5,000 151,980 21.2 -10%

Suisun shrew

Habitat 28,742 22,590 6,237 5,672 22,505 16,918 0 8 3,600-4,800 9

3,600-4,800 8,9

20,518-21,718 8,9 74.6 -79 -9-(-4%)

Birds Tricolored blackbird



Nesting habitat 24,036 14,372 4,104 3,420 19,932 10,952 0 8 17,900-26,800

17,370-26,870 8,9

28,852-37,752 8,9

76.2% - 80.8 101-163%

Foraging habitat: non agriculture 99,587 40,818 5,878 3,865 93,709 36,953 8,700 8 0 8,700 8 45,653 8,9 48.7 12%

Foraging habitat: agriculture 275,937 33,097 24,781 2,464 251,15

6 30,633 16,620-32,640 8 0 16,620-

32,640 8 47,253-63,273 8

18.8% - 25.2 43-91%

Total 399,560 88,287 34,763 9,749 364,797 78,538 25,320-

41,340 17,900-26,800

43,220-68,140 9

121,757-146,677 9

31.8% to 37.5 38-66%

Suisun song sparrow

Habitat 26,958 21,177 5,272 4,798 21,686 16,379 0 8 3,600-4,800 9

3,600-4,800 8,9

19,979-21,179 8,9

79.0% - 80.0 -6-0%

Yellow-breasted chat Primary Nesting and

Migratory Habitat 7,384 2,192 351 200 7,033 1,992 0 8 >2,000 >2,000 8 >3,993 8 44.2 >82%

Secondary Nesting and Migratory Habitat 5,530 1,896 468 335 5,062 1,561 0 8 <3,000 <3,000 8 <4,561 8 56.6 <141%

Suisun Marsh/Upper Yolo Bypass Nest and Migratory Habitat

1,256 933 230 204 1,026 729 0 8 0 0 8 729 8 71.0 -22%

Total 14,171 5,022 1,049 739 13,122 4,283 0 5,000 5,000 9,282 51.2 85% Least Bell's Vireo

Habitat 14,137 5,008 1,049 736 13,088 4,272 0 8 >2,000 >2,000 8 >6,272 8 41.6 >25% Western burrowing owl

High-value habitat 78,447 26,261 3,569 1,980 74,878 24,281 8,000 8 2,000 10,000 8 34,281 8 44.6 31% Moderate-value habitat 52,800 16,214 4,260 1,020 48,540 15,194 >3,900 8 0 >3,900 8 >19,094 8 39.3 >18

Low-value habitat 243,129 27,833 21,631 1,045 221,498 26,788 0 8,10 0 0 8,10 26,375 8,10 11.9 -5

Total 374,377 70,309 29,460 4,045 344,917 66,264 >11,900 8 2,000 >13,900 8 >78,978 8 22.8 >12

Western Yellow-billed Cucko Breeding Habitat 6,825 2,763 574 407 6,251 2,356 0 8 >1,000 >1,000 8 >3,356 8 46.8 >21 Migratory Habitat 4,890 1,325 228 151 4,662 1,174 0 8 0 0 8 1,174 8 25.2 -11

Total 11,715 4,088 802 558 10,913 3,530 0 >1,000 >1,000 >4,531 38.0 >11 California Least Tern 2

Habitat 86,242 18,080 46 64 86,196 18,016 0 8 >10,000->20,000 9

>10,000->20,000 9

>28,016->38,016 8,9

29.1 - 35.8 >54->110

Greater sandhill crane Roosting/Foraging

Habitat 11,829 6,743 0 0 11,829 6,743 0 320 320 7,063 58.1 0

Foraging Habitat 184,257 33,259 6,739 3,686 177,518 29,573 >4,800 0 >4,800 >34,373 8 19.4 >3

Total 196,086 40,002 6,739 3,686 189,347 36,316 >4,800 320 >5,120 >41,436 21.9 >4



1 Table 5-10. Summary of Conservation Provided for Covered Wildlife and Plant Species with Full BDCP Implementation

(i.e., conditions at the late long-term evaluation point) (continued)

Covered Species


Permanently Removed (acres) 2 [E =

A-C]Exten

t Remaining

[F = B-D]Remaining Existi

ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]

Percent Change in Extent of Protected


[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane

ntly Removed Protecte

d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

California black rail

Habitat 33,563 24,593 5,949 5,265 27,614

19,328 0 8 17,500-

26,400 9 17,500-

26,400 8,9 36,828-

45,728 8,9 81.6 - 84.7 50-86

California clapper rail

Habitat 7,895 5,013 327 318 7,568 4,694 0 8 3,600-4,800 9

3,600-4,800

8,294-9,494 8,9

74.3 - 76.8 67-89

Swainson’s hawk

Foraging habitat 436,417 75,743 37,552 6,828 398,8

65 68,91

5

20,020-36,040

8,10 0 20,020-

36,040 8,10 88,935-104,955

22.3 - 26.3 17-39

Nesting habitat 10,149 3,258 706 469 9,443 2,789 0 8 4,000 4,000 8 6,789 8 50.5 108

Total 446,566 79,001 38,258 7,297 408,3

08 71,70

4 20,020-36,040 4,000 24,020-

40,040 95,724-111,744

23.2 - 27.1 21-41

White-tailed kite

Breeding habitat 13,714 4,518 868 567 12,846 3,951 0 8 4,000 4,000 8 7,951 8 47.2 76

Foraging habitat 478,251

101,068 44,417 12,837 433,8

34 88,23

1

24,620-46,040

8,10 0 24,620-

46,040 8,10 112,851-134,271

26.0 - 30.9 12-33

Total 491,965

105,586 45,285 13,404 446,6

80 92,18

2 24,620-40,040 4,000 28,620-

50,040 120,802-142,222

26.8 - 31.6 14-35

Reptiles Giant Garter Snake

Aquatic Breeding, Foraging and Movement 19,824 5,725 565 321 19,25

9 5,404 >6,900 8 13,690-22,040

>20,590->28,940

>25,994->34,344

78.9 - 83.2 >354->500

Upland Aestivation and Movement

190,805 31,954 13,713 2,941 177,0

92 29,01

3 7,100 8 0 7,100 8 36,113 8 20.4 13

Total 210,629 37,679 14,278 3,262 196,3

51 34,41

7 >14,000 13,690-22,040

>27,690->36,040 9

>62,106->70,456 9

29.6 - 32.2 >65->87



Table 5-10. Summary of Conservation Provided for Covered Wildlife and Plant Species with Full BDCP Implementation (i.e., conditions at the late long-term evaluation point) (continued)

Covered Species



A-C]Exten

t Remaining


ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]



[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane


d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

Aquatic Breeding, Foraging and Movement (miles)

6,000 1,012 342 80 5,658 932 0 8 0 0 8 932 8 16.5 -8

Western pond turtle

Aquatic habitat 7 78,511 30,591 6,013 4,636 72,498

25,955 0 8 27,900-

46,800 27,900-

46,800 8,9 53,855-

72,755 8,9 53.6 - 61.0 76-138

Dispersal habitat 579,334

109,348 47,471 14,820 531,8

63 94,52

8 4,000 8 0 4,000 8 98,528 8 18.5 -10

Upland nesting and overwintering 54,880 19,738 4,317 2,010 50,56

3 17,72

8 >5,230 8 5,000 >10,230 8 >27,958 8 50.3 >42

Total 712,725

159,677 57,801 21,466 654,9

24 138,2

11 >9,230 32,900-51,800

>42,130->61,030 9

>180,341-

>199,241 9

26.2 - 30.0 >13->25%

Amphibians California red-legged frog

Aquatic habitat 117 4 1 0 117 4 3 8 0 3 8 7 8 6.0 81 Upland cover and

dispersal habitat 4,984 640 168 81 4,816 560 1,000 9 0 1,000 9 1,560 9 32.2 144

Dispersal habitat 19,572 151 663 13 18,909 138 0 8 0 0 8 138 8 0.7 -9

Total 24,673 795 832 94 23,841 701 1,003 0 1,003 1,704 7.1 114

Western spadefoot toad Aquatic Breeding

Habitat 6,790 4,256 48 9 6,742 4,246 300 200 500 4,746 68.4 12

Terrestrial Cover and Aestivation Habitat 14,353 5,071 464 150 13,88

9 4,921 8,400 8 500 8,900 8 13,821 8 96.1 173

Total 21,143 9,327 512 159 20,631 9,168 8,700 700 9,400 18,567 87.0 99




Covered Species



A-C]Exten

t Remaining


ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]



[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane


d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

Aquatic Breeding Habitat (miles) 41 11 0 0 41 11 0 0 0 11 26.8 -2

California tiger salamander Aquatic breeding habitat 6,772 4,255 42 9 6,730 4,246 300 200 500 4,746 68.5 12 Terrestrial Cover and

Aestivation Habitat 14,353 5,071 464 150 13,889 4,921 8,400 8 500 8,900 8 13,821 8 96.1 173

Total 21,125 9,327 506 159 20,619 9,167 8,700 700 9,400 18,567 87.1 99

Invertebrates Valley elderberry longhorn beetle

Riparian vegetation 17,130 5,310 1,102 727 16,028 4,583 0 8 5,000 5,000 8 9,583 8 45.6 80

Non-riparian channels and grasslands 16,022 4,168 620 276 15,40

2 3,893 0 81 0 0 8 3,893 8 25.3 -7

Total 33,152 9,478 1,722 1,003 31,430 8,476 0 5,000 5,000 13,476 37.0 42

Lange's metalmark butterfly Habitat 1,108 67 0 0 1,108 66 0 0 0 67 6.0 0

Vernal pool tadpole shrimp Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5% 0

Conservancy fairy shrimp Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Longhorn fairy shrimp Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Vernal pool fairy shrimp




Covered Species



A-C]Exten

t Remaining


ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]



[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane


d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Mid Valley fairy shrimp Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

California linderiella Vernal Pool Complex 6,821 4,319 42 9 6,779 4,310 300 200 500 4,810 68.9 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Plants Alkali milk-vetch var.

Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Heartscale Habitat 495 127 10 4 485 124 150 0 150 274 56.5 115

Brittlescale Habitat 495 127 10 4 485 124 150 0 150 274 56.5 115

San Joaquin spearscale Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Slough thistle Habitat 1,831 188 5 0 1,826 188 0 > 1,000 > 1,000 > 1,188 42.0 >532

Suisun thistle7

Habitat 1,129 869 636 579 493 290 08 3,600-4,8009

3,600-4,8009

3,890-5,090

95 - 96.2 347%-485

Soft bird’s-beak7




Covered Species



A-C]Exten

t Remaining


ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]



[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane


d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

Habitat 1,224 869 636 579 588 290 08 3,600-4,8009

3,600-4,8009

3,890-5,090

92.9 - 94.5 347%-485

Dwarf Downingia Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Delta button celery Habitat 3,344 270 25 1 3,319 269 > 100 > 1,000 > 1,100 > 1,369 31.6 >407

Boggs Lake hedge-hyssop Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Carquinez goldenbush Habitat 1,032 391 42 2 990 389 300 0 300 689 69.6 76

Delta tule pea

Habitat 5,948 3,699 1,137 1,076 4,811 2,623 0 16,970-26,4709

16,970-26,4709

19,593-29,093

90.0% - 93.0 430%-687

Legenere Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Heckard’s peppergrass Vernal pool Complex 6,959 4,380 88 30 6,870 4,350 300 200 500 4,850 68.6 11 Degraded Vernal Pool

Complex 2,493 683 5 0 2,488 683 0 0 0 683 27.5 0

Mason’s lilaeopsis 6,931 1,717 146 80 6,785 1,637 0 16,980-26,5609

16,980-26,5609

18,617-28,197

78.3 - 84.6 984-1,542

Habitat

Delta mudwort 6,931 1,717 146 80 6,785 1,637 0 16,980-26,5609

16,980-26,5609

18,617-28,197

78.3 - 84.6 984-1,542

Habitat




Covered Species



A-C]Exten

t Remaining


ng Protected

Habitat

[G] Protected

Under BDCP (acres)

[H] Restored

Under BDCP (acres)

[I = G+H]Total



Implementation

[L=(J-B)/B]



[A] Total

[B] Extent Protec

ted

[C] Total

[D] Permane


d

[J=F+I]Protecte

d

[K=(J/(E+H)]

Percent Protect

ed

Suisun Marsh aster 5,948 3,699 1,137 1,076 4,811 2,623 0 16,970-26,4709

16,970-26,4709

19,593-29,093

90.0 - 93.0 430-687

Habitat Side-flowering skullcap 2,495 701 37 12 2,458 689 0 0 0 689 28.0 -2

Habitat Caper-fruited tropidocarpum 1,345 21 0 0 1,345 21 > 100 0 > 100 > 121 9.0 >476

Habitat Contra Costa wallflower 19 17 0 0 19 17 0 0 0 17 89.5 0

Habitat Antioch Dunes evening primrose 19 17 0 0 19 17 0 0 0 17 89.5 0

Habitat 1. Permanent impacts represent those associated with construction of forebays, Intake facilities, permanent access roads, shaft locations, muck areas, levee setback

footprints, riparian restoration areas, nontidal marsh restoration and conservation hatcheries facilities 2. Tidal Perennial Aquatic impacts related to the intake right of ways have been removed as it is assumed that these would not pose an impact to this natural community.

Tidal restoration impacts were assessed based on areas expected to become desiccated based on RMA modeling results. 3. Impacts assessed for tidal marsh restoration reflect those incurred to tidal brackish emergent wetland habitat components expected to be desiccated based on RMA

modeling results. 4. Does not include removal of agricultural lands to restore 2,000 acres of grassland and 200 acres of vernal pools. These effects will be included in the next version of

this table. 5. Features in this category include the following conveyance features: Barge Unloading Facility, Control Structure Work Area, Intake Road Work Area, Intake Work

Area, Pipeline, Pipeline Work Area, Road Work, Borrow and Spoils sites, Area, Safe Haven Work Area, Temporary Access Road Work Area, Tunnel Work Area 6. Periodic impacts represent those associated with the periodic flooding of the Yolo Bypass and floodplain setbacks along the San Joaquin River. 7. Impacts assessed for tidal marsh restoration reflect those incurred to habitat that are expected to experience inundation and desiccation. 8. Does not include patches of these habitat types that are present on BDCP lands acquired for other purposes and that would be incidentally protected under BDCP. 9. As modeled in the hypothetical tidal habitat restorations, see Appendix Z [RMA tech #4 & SAIC memo]).

10. The mix of alfalfa, irrigated pasture, and other cultivated crops annually maintained under the BDCP will vary among years over the term of the BDCP depending on market drivers on growers with conservation easements.

1

Documents

CHAPTER 5. OVERVIEW OF THE EFFECTS ANALYSIS · Overview of the Effects Analysis Chapter 5 Bay Delta Conservation Plan November 18, 2010 Steering Committee Working Draft Page i