Draft Aquatic Resources Study Plan/Scope of Work

Juneau Hydropower Inc.

Sweetheart Lake Hydroelectric Project P-13563

April 2012

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Table of Contents 1.0 Introduction ..................................................................................................................................... 5

2.0 Aquatic Resources Study: Goals and Objectives ................................................................ 6

3.0 Aquatic Resources: Existing Information and Need for Information ........................... 8 3.1 Existing Information ..................................................................................................................................... 8 3.2 Need for Additional Information ......................................................................................................... 16 4.0 Anadromous and Tidewater Resource Study .................................................................. 19 4.1 Study Area ...................................................................................................................................................... 19 4.2 Field Study Design ...................................................................................................................................... 19 4.2.1 Study Component #1 – Anadromous Resource assessment, evaluation,

analysis and possible PM&E measures .......................................................................................................... 20 4.2.2 Study Component #2 – Tidewater Resource assessment, evaluation,

analysis and possible PM&E measures ............................................................................................................ 22

5.0 Freshwater Resources Study ................................................................................................ 24 5.1 Study Area ..................................................................................................................................................... 24 5.2 Field Study Design ..................................................................................................................................... 25 5.2.1 Study Component #1 – Sweetheart Lake Aquatic Survey assessment, evaluation, analysis and possible PM&E measures Resident Population spawn habitat Surveys ............... 25 5.2.2 Study Component #2 – Sweetheart Creek Aquatic Survey assessment, evaluation, analysis and possible PM&E measures .............................................................................................................. 29

6.0 Water Quantity and Water Quality Analysis and PM & E ............................................... 30

7.0 Agency Resource Management Goals ............................................................................................ 32 8.0 Project Nexus ................................................................................................................................. 33

9.0 Consistency with Generally Accepted Practices .............................................................. 33 9.1 Aquatic Resources ...................................................................................................................................... 34

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10.0 Schedule for Conducting the Study .................................................................................... 34 10.1 Anadromous and Tidewater Resources Study ............................................................................. 34 10.2 Freshwater Resources Study ................................................................................................................ 35 10.3 Field Logistics .............................................................................................................................................. 35 11.0 Provisions for Technical Review .................................................................................................. 36 11.1 Quality Control .......................................................................................................................................... 36 12.0 References ................................................................................................................................................. 37 Appendix A ADFG Sweetheart Lake 1953, 1954 Stocking Report ..................................... 41

Appendix B Agency Comment table .............................................................................................. 43 FIGURES & TABLES Figure 1. Proposed Project Boundary and Transmission Line Alternatives 5 Figure 2. Satellite Photo Sweetheart Lake facing Gilbert Bay 8 Figure 3. 1980 FEIS Gilbert Bay Holkam Bay Study Area 9 Figure 4. USGS 1958 Plan and Damsite 10 Figure 5. Satellite Photo of Sweetheart Creek 11 Figure 6. Satellite Photo of the upper end of Lower Sweetheart Lake 12 Figure 7. Satellite Photo of Lower Sweetheart Creek and Gilbert Bay 13 Figure 8. USFWS Sweetheart Flats wetland types 16 Figure 9. Sweetheart Lake and Creek Channel Type Layer 19 Figure 10. USFWS Wetlands in the upper vicinity of Sweetheart Lake 26 Table 1. ADFG Sweetheart Creek Anadromous stream identification ..... 11 Table 2. ADFG Mean Harvest of Commercial Shellfish in Gilbert Bay . 14 Table 3. ADFG Mean Harvest of Commercial Crab in Gilbert Bay ....... 14 Table 4. Freshwater Resources Study Schedule 35

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List of Acronyms

ADFG Alaska Department of Fish and Game ADNR Alaska Department of Natural Resources af Acre foot or feet AF Alluvial Fan Channel Type AKEPIC Alaska Exotic Plants Information Clearinghouse APLIC Avian Power Line Interaction Committee AWC Anadromous Waters Catalog BLM Bureau of Land Management BMP Best Management Practices °C Degrees Celsius cfs cubic feet per second cm centimeter °F Degrees Fahrenheit EA Environmental Assessment EFH Essential Fish Habitat EIS Environmental Impact Statement EPA Environmental Protection Agency FERC Federal Energy Regulatory Commission FEIS Final Environmental Impact Statement FP Flood Plain Channel Type ft feet GPS global positioning system GWh gigawatt hours JHI Juneau Hydropower Inc kWh kilowatt hours MW Megawatt MWh Megawatt hours NEPA National Environmental Policy Act NWI National Wetlands Inventory PAD Preliminary Application Document PM&E Protection, Mitigation and Enhancement Project Sweetheart Lake Hydroelectric Project SD2 Scoping Document 2 USACE U.S. Army Corps of Engineers USFS United States Department of Agriculture Forest Service USFWS U.S. Fish and Wildlife Service USGS U.S. Geological Survey

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1.0 Introduction

In December 2009, the Federal Energy Regulatory Commission (FERC) in Washington D.C. issued to Juneau Hydropower Inc. (JHI) a Preliminary Permit (Permit) for the Sweetheart Lake Hydroelectric Project (FERC No. 13563, Project). The Project would be located on the mainland approximately 30 miles southeast of the City of Juneau, Alaska (see Figure 7). The proposed Project consists of an intake structure at Lower Sweetheart Lake, a dam at Lower Sweetheart Lake, a power conduit consisting mostly of tunnels, and a steel penstock leading to a buried or partially buried powerhouse located above or adjacent to the barrier falls at Sweetheart Creek. An operators' house would be built either collocated at the power house or built away from the powerhouse and situated toward the dock infrastructure on Gilbert Bay. Transmission of electricity would occur either by a mix of submarine and overhead transmission traversing the west side of Gilbert Bay or through a submarine cable across Gilbert Bay to the Snettisham transmission line point of interconnection (Figure 1). The operational proposal includes a storage dam; the current proposal is to draw water from Lower Sweetheart Lake in such a way as to contain lake level fluctuations to 60 feet, with final drawdown prescriptions to be determined based on further economic and environmental considerations. During initial consultation and scoping, Project stakeholders including Alaska state and federal resource agencies indicated concern for potential Project effects on aquatic resources relative to Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay. This study plan is based on Project details provided in the JHI Preliminary Application Document (PAD) issued July 28, 2010, an initial agency meeting on October 28, 2012, scoping and site visits conducted September 7 and 8 2011, Scoping Document Two (SD2) issued on February 1, 2012 as well as agency comments and inputs subsequent to these activities. Documents, meeting videos, submissions, and study requests from Consultation and Scoping are available for review at; www.juneauhydro.com. This study plan responds to study requests and issues made during these activities, while outlining work to comply with federal laws and regulations. This Aquatics Study Plan (Plan) addresses the Lower Sweetheart Lake, Sweetheart Creek, southern Gilbert Bay and immediate area and associated facilities of the Project. The overall study goals and objectives are discussed in Section 2 of this Plan, and site specific objectives and associated methods are discussed in Sections 4, 5 and 6 of the plan. Aquatic resources data gathering, field surveys and planned analysis discussed in this Plan will be used by the ADFG and USFWS, the FERC and other state and federal resource agencies to help evaluate and resolve impacts of the Project prior to issuance of the Project license.

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Figure 1. Proposed Project Boundary and Transmission Line Alternatives.

2.0 Aquatic Resources Study: Goals and Objectives

In collaboration with existing information, the goal of the study effort described in this plan is to provide baseline information, which will inform an assessment of potential Project impacts on aquatic resources in the study report. The impact assessments will inform potential protection, mitigation, and enhancement measures to be presented in the draft and final License Applications. Overall goals and objectives were identified during development of the PAD, public comment, and FERC scoping for the License Application. The overall goals and objectives of this study are to provide supporting information which will provide the basis for an assessment of the potential resource impacts of the proposed Project. Overall goals and objectives are broken into two major elements: Aquatic Biological Resources and Water Quantity and Quality. Due to their interdependency overall goals and objectives are covered throughout the various study components described below as well as a separate Water Quality and Quantity section. Overall goals and objectives from the Aquatic Biological Resources and Water Quality and Quantity elements are taken directly from SD2 (Sections 4.2.2 and 4.2.3 respectively) and are listed below:

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Section 2.1 Aquatic Biological Resources

• Effects of project construction, operation, and maintenance (e.g., sedimentation,

disturbance, modification) on physical habitat of Lower Sweetheart Lake, Sweetheart Creek and Gilbert Bay and the effective areas of inundation (approximately 100 feet above the highwater mark).

• Effects of project operation and water level fluctuations on fish species and habitats in

Lower Sweetheart Lake.

• Effects of project operation, including alterations to existing flow regime and food web of Sweetheart Creek, on aquatic communities in Sweetheart Lake and Gilbert Bay.

• Effects of submarine transmission line construction on aquatic biological communities

in Gilbert Bay

• Effects, if any, of submarine transmission line construction on fish and shellfish communities in Gilbert Bay

• Effects of project construction and operation on marine mammals in Gilbert Bay and Port

Snettisham .

• The effects of project construction, operation, and maintenance on out migration of sockeye juveniles from Lower Sweetheart Lake.

• The effects to fish communities in Sweetheart Creek and Gilbert Bay from potentially

changing the survival rate of sockeye juveniles that outmigrate from Sweetheart Lake.

• The effects of raising the elevation of Sweetheart Lake on fisheries resources in Sweetheart Lake and spawning areas and creeks upstream of Sweetheart Lake.

• The effects of electromagnetic frequency from submerged transmission lines on aquatic

species in Gilbert Bay. Section 2.2 Water Quantity and Quality

• Effects of project construction, operation, and maintenance on nutrients, erosion,

sedimentation, and turbidity levels of Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay.

• Effects of project construction, operation, and maintenance on changes to nutrients, water temperature, dissolved oxygen, dissolved gas levels, and rock leachate of Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay.

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• Effects of contamination via accidental releases of fuels, lubricants, and other wastes from construction equipment, machinery and operations on Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay water quality.

• Effects of project construction and operation on Sweetheart Creek flows. As stated above these goals are interdependent and will be performed by close collaboration between JHI and its various contractors. The following Biological Aquatic Resource surveys for the Project are to provide existing baseline distribution and abundance information on target aquatic species and the determination of Essential Fish Habitat (EFH). In turn this information combined the findings from the Water Quantity and Quality studies and other engineering studies will be used to facilitate the FERC process.

3.0 Aquatic Resources: Existing Information and Need for Information

Figure 2. Satellite Photo Sweetheart Lake with Sweetheart Creek and Gilbert Bay to the right of the frame.

3.1 Existing Information Minor investigation of aquatic and fishery resources has been performed in the lower reaches of the Project vicinity under the USDA Forest Service Alaska Region Final Environmental Impact Statement- Proposed Recreational Development and Independent Timber Sale Gilbert Bay/Holkham Bay Area

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Southeast Alaska (Figure 3 ). Other work has been conducted by the ADFG in compiling data in relation to sockeye smolt stocking (Yanusz and Barto 1995), for editions of the Anadromous Fish Catalog, and in season anadromous escapement counts. Further, ADFG has detailed harvest records for fishery resources harvested in Gilbert Bay.

Figure 3. 1980 FEIS Gilbert Bay Holkam Bay Study Area

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In 1958, the United States Geological Service developed a Sweetheart Lake plan and Damsite in which topography as well as sounding readings of lake depth were made (Figure 4). JHI plans to use the USGS data for bathymetric purposes.

Figure 4. USGS 1958 Plan and Damsite for Lower and Upper Sweetheart Lakes Aquatic Resources.

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Little data exists on catch effort and abundance of rainbow trout in Lower Sweetheart Lake. This is not uncommon for Southeast Alpine lakes that are only accessible by float plane. No developed trails exist from tidewater to Lower Sweetheart Lake.

Existing fisheries and aquatic resources are discussed below relative to the following potentially-affected water bodies:

Sweetheart Creek

Figure 5. Satellite Photo of Sweetheart Creek ADFG 2006 Catalogue of Anadromous Fish Waters a listing of occurrence and distribution of Alaska anadromous fish indicates that chum (Oncorhychus keta) and pink salmon (O. gorbuscha) occur in Sweetheart Creek which is listed as Stream # 111-35-10200. Salmon in Sweetheart Creek do not migrate into Lower Sweetheart Lake because of a set of barrier cascades in Sweetheart Creek at the base of the falls. Due to slope and height restriction of these falls, spawning pink and chum salmon pool at the base of the falls in limited spawning habitat. Returning lake stocked sockeye (O. nerka) do not spawn, but supports an important local personal use fishery user group. Table 1. ADFG Sweetheart Creek Anadromous stream identification

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There have not been any known investigations or separate reports of indigenous trout populations in Sweetheart Creek. The falls elevating over a relative short distance and lack of intermittent pools likely create an inhospitable habitat for resident trout populations, but presence is unknown. There are anecdotal reports of sea run Dolly Varden (Salvelinus malma) and cutthroat trout (Oncorhynchus clarki ) exist below the falls as provided by the US Forest Service letter to JHI on November 3, 2009. Based on the several species of salmon spawning in Sweetheart Creek, it is possible that Dolly Varden and cutthroat predatory presence likely occurs while salmon are spawning below the barrier falls of Sweetheart Creek. Sweetheart Lake

Figure 6. Satellite Photo of the upper end of Lower Sweetheart Lake. Approximately 500,000 Sockeye fry are stocked annually in Sweetheart Lake from the Port Snettisham hatchery operated by DIPAC. According to DIPAC, averages of 2500 to 3000 adult sockeye are harvested annually from the personal use fishery. The outlet of the lake, Sweetheart Creek, cascades down a 500-foot fall before entering salt water. Investigations completed in 1993 indicated that only about 60% of sockeye smolts leaving the lake survived this drop (Yanusz and Barto 1994). JHI conversations with DIPAC personnel indicate that the survival rate of out migrating salmon smolt could be lower than 50%. The first adults of the stocking program returned in 1993. Speel Lake stock is used for the fry stocking

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put and take fishery at Sweetheart Lake and Creek. This stocking program created a successful and popular personal use fishery at the base of the barrier falls at Sweetheart Creek. JHI has researched two other Southeast Alaska salmon outmigration systems developed and utilized by two hatchery operations. The Deer Lake Hatchery by Northern Southeast Regional Aquaculture Association (NSRAA) utilizes a coho outmigration system ( http://www.nsraa.org/Deer_Lake.html) . The Spiridon Lake program operated by Kodiak Regional Aquaculture Association supports a sockeye salmon outmigration system. ( http://www.adfg.alaska.gov/index.cfm?adfg=CommercialKodiakresearch.project&id=10 ) JHI will propose to emplace similar “smolt line” system tailored to Sweetheart Lake and Sweetheart Creek. The intention of the improved downstream fish passage method should substantially decrease mortality of outgoing sockeye smolts and will therefore, in theory, increase returning numbers of adult sockeye for the popular personal use fishery that takes place below the barrier falls of Sweetheart Creek. According to ADFG notes, studies prior to sockeye enhancement, phone conversations, and memos, it is apparent that Lower Sweetheart Lake was stocked with rainbow trout in 1954 and or 1955 (Appendix A). This created a naturalized spawning resident population of trout living in the lake. Based on evidence occurring in Deer Lake operated by NSRAA which has a similar coho salmon stocking program at Sweetheart Lake, there is a likelihood that the sockeye fry stocking has contributed feed and likely increased the size and population of 1950 era introduced trout. Landlocked dolly varden are also reported to inhabit the lake. Sweetheart Flats/ Gilbert Bay

Figure 7. Satellite Photo of Lower Sweetheart Creek and Gilbert Bay

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These marine areas support a diverse community of fish species including salmon and several species of ground fish along with shellfish (see Figure 6). Personal use fishers target pink salmon and Sockeye salmon, primarily those focusing on the DIPAC stocked Sockeye fishery in late July to mid- August. There is also a personal use and commercial Dungeness crab fishery for Dungeness Crab in Gilbert Bay and possibly some shrimp harvesting in the vicinity of the proposed submarine cable. Gilbert Bay represents ADFG Statistical Area 111-35 for shellfish and crab purposes (Table 2, Table 3). Table 2. ADFG Mean Harvest of Commercial Shrimp in Gilbert Bay

Pounds Permits Pounds Permits Pounds Permits Pounds Permits

2,709 9 29,850 3 8,433 3 527 2Source ADF&G Commercial Fisheries Division 2010

Mean harvest (pounds) and effort (# permits) for commercial shrimp fisheries in Gilbert Bay, Subdistrict 111-35, for 2000/01-2009/10 seasons. Seasons are grouped for reporting purposes to avoid disclosure of confidential information where less than 3 permit holders were participating.

Coonstripe Pink shrimp Sidestripe shrimp Spot shrimp

Table 3. ADFG Mean Harvest of Commercial Crab in Gilbert Bay

Pounds Permits Pounds Permits Pounds Permits Pounds Permits

14,678 8 9 1 4,463 12 2,603 9Source ADF&G Commercial Fisheries Division 2010

Red king crab Bairdi tanner Blue king crab Dungeness crab

Mean harvest (pounds) and effort (# permits) for commercial crab fisheries in Gilbert Bay, Subdistrict 111-35, for 2000/01-2009/10 seasons. Seasons are grouped for reporting purposes to avoid disclosure of confidential information where less than 3 permit holders were participating.

The Project Area contains four potentially affected water bodies: Upper Sweetheart Lake, Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay.

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Potentially Affected Waterbodies

Upper Sweetheart Lake. Upper Sweetheart Lake is located at an elevation of 1865 feet (relative to low mean sea level), 1321 feet higher than Lower Sweetheart Lake (the two lakes are connected by a stream). The raising of Lower Sweetheart Lake by 85 feet should not affect Upper Sweetheart Lake and therefore JHI in agreement with ADFG PAD comments is not anticipating potential impacts and is not anticipating study needs for Upper Sweetheart Lake.

Lower Sweetheart Lake. Lower Sweetheart Lake rests at 544 ft elevation above sea level and has 1257 acres with 250,000 acre feet. Lower Sweetheart Lake (herein referred to as Sweetheart Lake) potentially supports Dolly Varden (assumed to be native) and a known self-sustaining population of rainbow trout (stocked in 1953 and 1954 with a total 60,000 fry-see Appendix A). Sweetheart Lake is stocked annually with sockeye fry from Douglas Island Pink and Chum (DIPAC) hatchery at Port Snettisham. These fish rear in the lake for one year (sometimes two) before outmigrating down Sweetheart Creek into Gilbert Bay. As adults, they return to Sweetheart Creek, providing a very popular personal use fishery for Juneau residents. These adult sockeye do not migrate to Sweetheart Lake because of barrier falls and do not reproduce.

Sweetheart Creek. Sweetheart Creek has been specified as an anadromous fish stream under AS 41.14.870 as stream number 111-35-10200 and is catalogued for pink salmon and chum salmon. This anadromous reach is also known to support Dolly Varden and cutthroat trout. It is understood with ADFG that the anadromous reach may not extend upstream as far as indicated in the Anadromous Waters Catalog due to a barrier falls. ADFG has committed to work with JHI to identify the upper extent of the anadromous reach. It is unknown whether Sweetheart Creek supports resident fish in the stream reach between this barrier falls and Sweetheart Lake.

Gilbert Bay and Port Snettisham. Gilbert Bay and Port Snettisham provide sport, personal use, and commercial fishing opportunities for salmonids, groundfish, and shellfish (Table 1, Table 2). This area also provides recreational opportunities such as wildlife viewing (e.g., humpback whales and bears), and Gilbert Bay is used as an anchorage for vessels traveling in Stephens Passage.

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Figure 8. USFWS Sweetheart Flats Estuarine Areas.

3.2 Need for Additional Information

The Sweetheart Lake Hydroelectric Project, based on agency reviews and comments related to the PAD, requires additional information for environmental assessment purposes as a component of FERC licensing. Agency written and verbal comments documented in writing and videotaped at the Initial Agency Meeting and at the agency and public scoping meetings, scoping comments and resulting scoping document provide the basis for the Aquatic Resources Study needs. Study requirements are proposed to meet project potential impacts on aquatic resources.

Sweetheart Lake and Inflow Tributaries.

The Sweetheart Lake Basin is dominated by rock and ice landforms with alpine tundra and coastal rainforest and limited occurrences of muskeg in the remaining areas. The lake is deep with a reported depth of 430 feet and has precipitous shorelines.

The proposed project would raise the natural elevation of Sweetheart Lake from 544 feet to 629 feet by damming the outlet to Sweetheart Creek. This dam would block resident fish from accessing the outlet stream and prevent sockeye smolts from naturally outmigrating down Sweetheart Creek to Gilbert Bay. Outlet streams sometimes provide important spawning, rearing, and feeding habitats. ADFG reports that Rainbow trout have been observed spawning in the outlet to Sweetheart Creek. Raising Sweetheart Lake 85 feet would inundate existing littoral zone and inlet stream habitats. Additionally, it is possible that entrainment and impingement at the penstock intake could cause fish mortality.

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Proposed project operations would fluctuate the elevation of the newly impounded reservoir 60 feet annually. Unnaturally large and unseasonal fluctuations in reservoir levels can 1) impact the ability of fish to access inlet stream habitats used for spawning, rearing, and feeding during low reservoir levels, 2) inundate these habitats during high reservoir levels, 3) alter the morphology and habitat conditions (e.g., substrate composition) of inlet streams, 4) alter littoral, shoreline, and riparian zone habitats within the zone of inundation, and 5) impact recreational and aesthetic values.

A preliminary evaluation of stream channel types, based on Forest Service GIS data, indicates that some spawning habitat for resident rainbow trout and dolly varden char in Sweetheart Lake Basin could be inundated by elevation of the lake surface to 629 feet as proposed. Figure 10 (see below) illustrates that much of the accessible flood-plain channel type and most of the alluvial-fan and moderate-mixed channel types lie below 600 feet, and would be seasonally inundated by project operations. These channel types often provide important spawning habitat, while steeper, typically rockier reaches usually offer little or none. However, the inflow tributaries will be evaluated as seasonal reservoir inundation may also create new spawning habitats.

Sweetheart Creek Bypass Reach. For the purpose of this Aquatics Resource Study, it is assumed that the tailrace will discharge at the base of the downstream most barrier falls (i.e. at the upper extent of the anadromous reach). Proposed project operations would significantly reduce flows in the bypass reach. ADFG suggests that stream temperatures could also be impacted depending on the depth in the reservoir from which flows are released downstream. Because of the dam and reduced flows, the recruitment and movement of sediment and woody debris could be reduced; potentially impacting channel morphology and instream habitat conditions of the bypass reach. It is not known if the bypass reach supports resident fish and if so, to what frequency or distribution.

Sweetheart Creek Anadromous Reach. Proposed project operations would alter instream flows and stream temperatures in the anadromous reach, possibly impacting (positively or negatively) spawning, rearing, and incubation of anadromous fish. Altered flows could also impact recreational uses of the anadromous reach; in this case, the sockeye personal use fishery (e.g., high flows could prevent access for fishing). Because of the dam and reduced flows in the bypass reach, the recruitment and movement of sediment and woody debris could be reduced, potentially impacting channel morphology and instream habitat conditions of the anadromous reach.

Unnaturally rapid changes in flow resulting from project operations (tailrace discharges) could create unstable instream habitat conditions and impact fish populations and other aquatic organisms. Examples of impacts include stranding of fry, juvenile and adult fishes, dewatering of redds, and changes in fish passage and movements. Rapid changes in flow could also impact the sockeye personal use fishery.

Gilbert Bay and Port Snettisham. The installation, operation, and maintenance of the proposed submarine transmission cable could impact salmonids, groundfish, and shellfish resources in Gilbert Bay and Port Snettisham, and the sport, personal use, and commercial fisheries targeting these marine resources. For example, the submarine cable could interfere with fishing gear and could pose hazards for vessels anchoring in the vicinity. Construction, operation, and maintenance of proposed or potential project access facilities (roads, docks, helicopter landing areas, and transshipment centers) could affect water quality and sedimentation in Gilbert Bay.

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As proposed, the project could alter the timing, quantity, and temperature of freshwater inputs from Sweetheart Creek into Gilbert Bay, potentially impacting marine resources in the area. For example, changes in the timing and quantity of freshwater inputs could affect water column stratification and the spring phytoplankton bloom, potentially impacting the survival of rearing crab and shrimp (the spring phytoplankton bloom provides the important first feeding for newly hatching crab and shrimp).

Anadromous and Resident Fish Habitat

It has been recommended that JHI identify the resident and anadromous species and characterize life stage timing in the project area; inventory and map stream habitats and determine how habitat would be affected by changing flows; identify and characterize existing and proposed fish passage barriers; and examine how project operations would affect instream flow conditions, including the amount of flow and water quality. Ramping of tailrace discharge associated with power house operation will be evaluated to predict the effects of project operations on habitat availability, quality, and use. Continuous stream flow gauging shall be conducted in the anadromous reach for at least until license is received and possibly up to five years to adequately characterize the stream flow in Sweetheart Creek. It should be noted that there is a large data set of stream gaging activity conducted by the USGS in Sweetheart Creek. New data combined with historical data will allow for evaluation of alternatives that could reduce project impacts on fish populations. Stream flow data and habitat information in combination with detailed operation plans and ramping rates are necessary to design adequate in-stream flow requirements for the anadromous reach.

A preliminary evaluation of stream channel types, based on Forest Service GIS data, indicates that some spawning habitat for resident rainbow trout and any Dolly Varden char in Sweetheart Lake could be inundated by elevation of the lake surface to 629 feet as proposed. Figure 10, Sweetheart Channel Type Layer illustrates that much of the accessible flood-plain (FP) channel type and most of the alluvial-fan (AF), low gradient contained (LC) and moderate-mixed channel types lie below 600 feet, and would be inundated by project operations. These channel types often provide important spawning habitat, while steeper, typically rockier reaches usually offer little or none. However, it is possible the timing of the inundation that new spawning areas are created.

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Figure 9. Sweetheart Lake and Creek Channel Type Layer.

4.0 Anadromous and Tidewater Resource Study

4.1 Study Area The study area includes the area on east side of Gilbert Bay and the North side of Sweetheart Creek in the general facility of the proposed Project facilities and the potential overland transmission route to the west. The study area includes all proposed Project facilities along Sweetheart Creek to the barrier falls within and proposed transmission line routing (Figure 1).

4.2 Field Study Design

The Anadromous and Tidewater Resources Study is comprised of two components that will include:

• Study Component #1- Anadromous Resource assessment, evaluation, analysis and PM&E.

• Study Component #2- Tidewater Resource assessment, evaluation, analysis and PM&E.

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4.2.1 Study Component #1 – Anadromous Resource assessment, evaluation, analysis and possible PM&E measures.

Sweetheart Creek Anadromous Reach

Site specific assessment objectives in the Sweetheart Creek Anadromous Reach will allow researchers and agency personnel evaluate possible project effects and include the following:

• Identify all resident and anadromous species and characterize life stage timing in the project area: Assess baseline presence, distribution, and periodicity (seasonal use of habitat for spawning, incubation, rearing, and passage) by species and life stage.

• Inventory and map existing stream habitat.

• Organize existing and develop baseline hydrology and water temperature information that complies with USGS standards in order to assess the potential impacts. These data will be used to estimate mean daily, monthly, and annual flows, as well as monthly duration flows in Sweetheart Creek and seasonal stage elevations of Sweetheart Lake

• From the evaluation of the data listed above; develop relations between seasonal instream flows, stream temperatures on habitat quantity and quality (for spawning, incubation, rearing, and migration). From this information JHI and applicable agencies will be able to:

• Determine if ramping rates are needed for tailrace discharges and develop said tailrace discharges, ramping rates and instream flows

• Develop plans for protecting instream flows for fish during emergency and routine maintenance shutdowns of project operations.

• Identify, characterize, and evaluate existing and proposed fish passage barriers.

Based on the baseline data and evaluation of the data possible mitigation and enhancement objectives in the Anadromous Reach may be to:

• Develop and suggest infrastructure and operational plan recommendations for protecting instream flows (including ramping rates and tailrace discharges) for fish during operations as well as for emergency and routine maintenance shutdowns of project operations.

• Develop and suggest infrastructure recommendations for tail race design and construction to increase anadromous salmon spawning habitat and life cycle enhancement.

Methods of Study

In order to identify all resident and anadromous species and characterize life stage timing in the Anadromous Reach researchers will assess baseline presence, distribution, and periodicity (seasonal use of habitat for spawning, incubation, rearing, and passage) by species and life stage. JHI has begun to

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develop baseline abundance, distribution and periodicity using available ADFG escapement data for the Sweetheart Creek . As this data was originally designed for salmon escapement purposes it will be used as a timeline basis supplemental foot surveys supplement to better describe fish timing and use. During these surveys species other than salmon to include, but not be limited to, Dolly Varden, cutthroat trout and steelhead trout will also be recorded.

During these surveys fish numbers by species, life stage and habitat usage will be documented on stream habitat maps as described below. Preformed data sheets or similar data recording techniques (i.e.

. Trimble) will be used in conjunction with the maps and will include the following information;

• Number of fish by species and life stage

• GPS location.

• Time of day (Stop and Start times)

• General weather condition

• Water temperature

• Relation of observation time to tide status and gage height

• Water transparency

• Activity (actively moving upstream, milling, exhibiting spawning behavior, etc.)

• Location of fish in the stream (i.e., are they concentrated in a pool or run, or are they spread evenly throughout the stream).

With these data sources (as well as other described later) JHI will develop baseline abundance, distribution and periodicity by specie and life cycle stages that will be suitable for later analysis on how proposed stream flow changes would affect habitat (See Below).

In order to inventory and map existing stream habitat and fish use of this habitat researchers will use detailed USFS satellite photos (1 Meter resolution) to initially inventory and map existing streams and channels. Foot surveys will be performed to identify, verify and photodocument stream habitat. A series of overlapping photos will be taken with a digital camera along the anadromous reach of Sweetheart Creek and labeled with the current stream gage level. This information will be used to update and add detail to existing maps as studies progress. These maps (as well as other methods described below) will be utilized during field surveys to document fish locations and habitat usage in relation to timing, life stage, and flows for later reference.

JHI will utilize historical and current stream flow data (from JHI continuous stream gage measurements) for instream flows as well as contemporary stream and vertical lake array temperature data (See below) to provide an appropriate model to provide a spectrum of proper water levels and stream temperatures. Continuous recording stream gages were installed at the outlet of Sweetheart Lake and in the anadromous reach of Sweetheart Creek. These stream gages comply with standards established by the USGS and

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record stage at 15-minute intervals. Discharge measurements and rating curves will comply with USGS standards. The JHI stream gage contractor will insure that these requirements are met and that data will be made available and shared with JHI aquatics contractors and consulting agencies. Stream gages and temperature loggers will be operated during and following construction phases for the life of the project for baseline, evaluation, and monitoring purposes.

Taking into account annual, diurnal, other naturally occurring hydrologic events (ex. rainfall), data from gages and temperature loggers will be used to estimate mean daily, monthly, and annual flows, as well as monthly duration flows in Sweetheart Creek and seasonal stage elevations of Sweetheart Lake. Similarly, JHI will determine if ramping rates are needed for tailrace discharges in consultation with appropriate agencies. If so determined, suggested ramping rates that identify and mitigate discharge issues related to rapid increase or decrease of flows similar to those developed by the Washington Department of Fish and Wildlife (WDFW), Technical Report Number 119 will be developed. Likewise JHI will develop plans for protecting instream flows for fish during emergency and routine maintenance shutdowns of project operations. These plans may include, but not be limited to, powerhouse and other bypass considerations to be incorporated in infrastructure design.

Water bottle testing before, during and after construction will be performed in order to ensure proper quality of water (in particular turbidity) for spawning, incubation, rearing and migration. By incorporating Best Management Practices (BMP’s) along with Water bottle testing before, during, and after construction JHI will ensure proper quality of water (in particular turbidity) for spawning, incubation, rearing and migration.

JHI does not propose to install any fish passage barriers in the anadromous reach except at the outtake of the tailrace head. Therefore in order to identify and characterize existing and proposed fish passage barriers JHI will identify, characterize and photograph existing fish passage barriers. Independently determine and coordinate with JHI stream gage contractor specific GPS grid coordinates and elevation of base of barrier falls. JHI will coordinate with ADFG habitat staff and will follow nomination guidelines for all possible inclusions or changes to the Anadromous Waters Catalog (ADFG 2009a)

After compiling and evaluating the data from the studies describe above, JHI in consultation with the appropriate agencies will:

• Develop and suggest infrastructure and operational plan recommendations for protecting instream flows for fish during operations as well as for emergency and routine maintenance shutdowns of project operations.

• Develop and suggest infrastructure recommendations for tail race design and construction to increase anadromous salmon spawning habitat and life cycle enhancement. Construction considerations in tailrace design and construction have been shown to have positive effects on anadromous salmon populations (Greeley A.W. 1985).

• Develop and implicate a plan for proper water quality using BMP’s and water bottle testing to ensure proper water quality (in particular turbidity) for spawning, incubation, rearing and migration.

• Catalog and characterize current and possible fish passage barriers.

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In summary JHI will develop baseline fisheries periodicity and habitat use data. Use this fisheries and habitat data along with hydrologic data, existing literature, agency consultation, and BMP’s in order to develop plans that will ensure proper fisheries management during and after construction of project features.

4.2.2 Study Component #2 – Tidewater Resource assessment, evaluation, analysis and possible PM&E measures.

Site specific assessment objectives in the Gilbert Bay Study Area will allow researchers and agency personnel evaluate possible project effects and include the following:

• Evaluate the potential impacts of constructing, operating and maintaining the proposed project access facilities (roads, docks, and infrastructure) on water quality and sedimentation in Gilbert Bay.

• Evaluate how the timing, quantity, and temperature of freshwater inputs from Sweetheart Creek into Gilbert Bay will change under proposed project operations.

• Evaluate the potential impacts of altering the timing, quantity, and temperature of freshwater inputs from Sweetheart Creek into Gilbert Bay on marine resources in the area.

• Evaluate the potential impacts of installing, operating, and maintaining the proposed submarine transmission cable segments on 1) salmonids, groundfish, and shellfish resources in Gilbert Bay and Port Snettisham, and 2) the sport, personal use, and commercial fisheries targeting these marine resources.

• Analyze project related relationships affecting tidewater resources and determine possible protection, mitigation and enhancement measures. Develop recommendations for PM&E measures as appropriate.

Methods of Study

JHI will evaluate the potential impacts of constructing, operating and maintaining the proposed project access facilities (roads, docks, and infrastructure) on water quality and sedimentation in Gilbert Bay. To complete this objective JHI will conduct desktop research and outline generally accepted construction and operational practices for the construction, operations and maintenance of infrastructure in a woodland and marine habitat. During this desktop process specific attention will be paid towards mitigating impacts and changes in the sedimentation of Gilbert Bay that may occur from the Sweetheart Lake Hydroelectric Project.

JHI will research and determine if there are impacts and to what degree of those impacts related to the timing, quantity and temperature of freshwater inputs from Sweetheart Creek to Gilbert Bay on marine resources in the area based upon proposed range of operational levels. To evaluate this potential impact, JHI and its contractors will compare historical USGS data with present water flows and relate them to proposed water flow operations by comparing pre project seasonal hydrographs versus proposed post

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project seasonal hydrographs. Using historical data (Yanusz and Barto 1994), data gathered during the study process (from temperature loggers, and water bottle testing), and information provided by other hydropower projects JHI will evaluate the potential effects that the proposed reservoir elevations will have on the timing, quantity, and temperature of freshwater inputs from Sweetheart Creek into Gilbert Bay have on marine resources in the area. In particular JHI will take into consideration the effects of water quality and quantity on water column stratification in relation the spring plankton bloom and in consultation with applicable agencies determine if and what measures are applicable.

JHI will use desk research from previous studies to evaluate the potential impacts of installing, operating, and maintaining the proposed submarine transmission cable segments on 1) salmonids, groundfish, and shellfish resources in Gilbert Bay and Port Snettisham, and 2) the sport, personal use, and commercial fisheries targeting these marine resources. Southeast Alaska has many electrical transmission cables (Skagway to Haines and Petersburg to Wrangell) and fiber optic cable (GCI Southeast Alaska) to use for comparison in order to evaluate potential impact on aquatic resources. JHI will examine the effects from these and other applicable projects and relate this information to how transmission cables in Gilbert Bay and Port Snettisham may affect the resources in the Project area. If impacts are unavoidable, determine suggested measures that could be undertaken to protect, mitigate and potentially enhance aquatic resources within the Gilbert Bay tidewater area.

5.0 Freshwater Aquatic Biological Resources Study

The Freshwater Aquatic Resources Study is comprised of two components that will include:

• Study Component #1 – Sweetheart Lake and Inflow Tributaries Aquatic Survey assessment, evaluation, analysis and possible PM&E measures

• Study Component #2 – Sweetheart Creek Bypass Reach Aquatic Survey assessment, evaluation, analysis and possible PM&E measures

5.1 Study Area

The Freshwater study area includes the area surrounding Lower Sweetheart Lake and Inflow Tributaries (including those potentially affected by the proposed inundation zone) and the Sweetheart Creek areas above the lowest barrier to fish passage upstream to the Project dam location ( those areas not described in the Anadromous Reach section).

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5.1 Field Study Design

5.2.1 Study Component #1 – Sweetheart Lake and Inflow Tributaries Aquatic Survey assessment, evaluation, analysis and possible PM&E measures

Lower Sweetheart Lake and Inlet Drainages

Site specific assessment objectives in the Lower Sweetheart Lake and Sweetheart Creek non-anadromous Reaches will allow researchers and agency personnel evaluate possible project effects, before during and after construction. Based on initial scoping and consultation these objectives include:

• Document baseline population characteristics, seasonal movements, and seasonal habitat use of resident species and characterize life stage timing in Lower Sweetheart Lake and its inlet and outlet streams. In particular conduct on-site studies to document location and extent of spawning habitat for trout and char populations in Sweetheart Lake.

• Inventory, quantify, describe, and map stream existing lake (including littoral) and inlet stream habitats and evaluate how habitat would be affected by changing flows and reservoir levels (in particular spawning habitats). In particular Flood Plain, Alluvial-fan, and moderate mixed channel types that lie below 629 feet that would be inundated by project operations will be examined for pre and post Project effects.

• Assess the potential impacts of project-induced seasonal reservoir fluctuations on spawning and rearing habitats in inlet streams, including impacts on channel morphology and substrate conditions.

• Assess the ability of fish to access inlet streams in relation to reservoir stage, particularly during spawning periods.

• Evaluate water temperatures at the proposed project intake in relation to reservoir stage:

• Evaluate the potential for fish entrainment and impingement at the project intake and corresponding protection and mitigation:

• Identify and characterize existing and proposed fish passage barriers. Consider design of pre-existing downstream passage and evaluate downstream passage facilities for sockeye smolt.

• Examine how project operations would affect instream flow conditions, including the amount of flow and water quality.

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Figure 10. USFWS Wetlands in the upper vicinity of Sweetheart Lake.

Method

In order to document baseline population characteristics, seasonal movements, and seasonal habitat use resident species and characterize life stage timing in Lower Sweetheart Lake, its inlet tributaries, and its outlet (to the area represented by the by-pass reach described below) JHI and its contractors will conduct on-site studies. In particular these studies will identify document location and extent of spawning habitats and spawn timing for resident rainbow trout and any resident Dolly Varden. Along with this JHI and its contractors will inventory and map stream habitats in order to evaluate how habitat would be affected by changing flows and reservoir levels.

In order to identify all resident species and characterize life stage timing in Lower Sweetheart Lake, its inlet tributaries, and its outlet researchers will assess baseline presence, distribution, and periodicity (seasonal use of habitat for spawning, incubation, rearing, and passage) by species and life stage. JHI has begun to develop baseline abundance, distribution and periodicity through limited trapping and emplacement of temperature loggers in 2011. During these surveys Dolly Varden and Rainbow Trout were the only species encountered and studies will focus on these species.

JHI and its contractors will deploy a multiple approach to determine Sweetheart Lake population characteristics utilizing both visual observation methods and active capture. Due to annual abundance of Sockeye fry and smolt, JHI will not be conducting a sonar study as the sonar will not differentiate between small sockeye and other resident species.

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Visual Observation methods will include boat foot, and snorkel surveys were applicable. Snorkel surveys will be used in the inlet tributaries wherever water depth, velocity, or other natural factors do not preclude their use, and in particular for documenting spawning fish. Wherever stream conditions allow surveys will be conducted in an upstream manner using generally accepted methods (Northcote and Wilkie 1963, Thurow R.F. 1994).

During these surveys fish numbers by species, life stage and habitat usage will be documented on stream habitat maps as described below. Preformed data sheets or similar data recording techniques will be used in conjunction with the maps and will include the following information;

• Number of fish by species and life stage

• GPS location.

• Time of day (Stop and Start times)

• General weather condition

• Water temperature

• Water transparency

• Activity (actively moving upstream, milling, exhibiting spawning behavior, etc.)

• Location of fish in the stream (i.e., are they concentrated in a pool or run, or are they spread evenly throughout the stream).

Documented spawning areas will be further characterized by performing substrate analysis suing appropriate methods (USDA 2001). After on-site studies to document location and extent of pre and post project spawning habitat for trout and char populations, Project alternatives that would reduce impacts to this critical habitat will be investigated.

For capture methods JHI will engage in using, rod and real, minnow traps, and small mesh hoop nets in these areas to determine resident rearing usage, current limits of fish distribution, and determine presence in various areas. For all methods two preformed data sheets will be utilized. Data recorded for each fish will include sample number, fork length, gear type, and trap or rod and real session number, will be recorded. Other comments including but not limited to mortality status, old or new tag or other scars, physical condition, etc. will also be recorded were applicable. Location (GPS), catch and the number of gear units (rod and reel and trap hours) for each gear type will be recorded on trap catch forms and location will also be recorded on maps or aerial photos.

With these data sources (as well as other described later) JHI will develop baseline abundance, distribution and periodicity by specie and life cycle stages that will be suitable for later analysis on how proposed stream flow changes would affect habitat (See Below).

JHI and its contractors will use USFS satellite photos (1 Meter resolution), current channel class and wetlands maps to identify all streams and potential habitat in the Lower Sweetheart Lake Basin. Flood

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plain, alluvial-fan and moderate-mixed channel types that lie below 600 feet that would be inundated by project operations which are known to support resident fish species will be of particular interest. Further detail will be added to these maps during surveys as the studies progress. These maps will serve as a platform to catalogue, quantify and describe fish observations and the existing littoral zone and inlet stream habitats that will be inundated. As well JHI and its contractors quantify and describe the littoral zone and inlet stream habitats that will be created with the proposed increase in elevations due to the project reservoir. Descriptions will include channels class and morphology and substrate where applicable

To do this JHI will conduct on-site studies to document through description and digitally photograph each stream up to a 100 ft elevation above the current lake level of 544 feet. JHI will determine and register altitude with a GPS altimeter or other measuring device to identify what the available habitat will be with lake fluctuations that will occur during hydropower operations. This potential available habitat will then be analyzed for habitat suitability during various life stages by the species and season. JHI will review and research published information on how reservoir fluctuations potentially impact the spawning and rearing habitats in inlet streams. Desktop research will include reviewing similar reviews at Southeast Alaska hydropower developments. Using these data sources and current channel morphology and substrate conditions JHI will evaluate quality and quantity of available habitats during proposed project operations.

JHI and its contractors will assess the ability of fish to access inlet streams in relation to reservoir lake levels with specific attention to the spawning periods of resident species. JHI will review each stream inlet and determine slope, estimated flows and determine if fish passages barriers exist along the reach of the stream in the inundated area and those areas immediately above the inundated lake levels. This will allow JHI to assess the potential impacts of project-induced seasonal reservoir fluctuations on access to spawning and rearing habitats in inlet streams and the impacts on channel morphology and substrate conditions,

In order to evaluate water temperatures at the proposed project intake in relation to reservoir stage JHI will place an anchored temperature gauge in the area of the proposed intake. An Onset brand data logger that takes intermittent readings over the study period will be utilized, and JHI will photograph the buoy and anchor system and document type of data measuring device and data logger. In addition JHI will evaluate existing water temperature information (Yanusz and Barto 1994).

JHI will evaluate the potential for fish entrainment and impingement at the project intake by reviewing the screens and intakes at other hydropower reservoirs as well as desk study by reviewing current generally accepted practices. Species and life stages found to be in the vicinity of the proposed intakes during field studies and there swimming speed versus the velocity of the water vortex created by the proposed intake will be taken into consideration when investigating corresponding protection and mitigation. A fish screen system will be considered to prevent entrainment and JHI will incorporate in its study the suggested work of Bryan Nordlund, Designing Fish Screens for Fish Protection at Water Diversions, NMFS 1996.

In order to avoid significant impacts on out-migrating sockeye smolt, JHI will identify and outline salmon outmigration systems. This will include intake as well as conveyance. Of particular interest are the Deer Lake system which is designed for coho and the Spiridon Lake system which is designed for Sockeye. At this time JHI proposes to install a "smolt line" similar to the one used at Deer Lake Hatchery by Northern

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Southeast Regional Aquaculture Association to deliver coho smolts from Deer Lake to saltwater due to terrain similarities. JHI will also incorporate design considerations used in the Spiridon Lake “sockeye smolt line due to the less hardy characteristics of this species. The JHI PAD states that this downstream fish passage method should substantially decrease mortality of outmigrating sockeye smolts and thereby increase the number of adult sockeye returning to Sweetheart Creek. It should be noted that the coho smolt at Deer Lake migrate to the outlet stream where they are intercepted by the smolt line. Sockeye smolt in Sweetheart Lake won't have access to the outlet stream once the project is built. Consequently, the sockeye smolt line will have to originate in the lake, necessitating a different design for attracting and intercepting the smolts than that used at Deer Lake. Successful salmonoid intake systems have been designed built whereby JHI will review currently used technologies. (Donohue, Kerry, Michael Jenkins Jr., Richard Riker, Vince Rybel, and Walter Bennett, “Retrofitting Existing Hydropower Intake Nearly 300 Feet Deep,” Proceedings of HydroVision International 2011), PennWell Corp., Tulsa, Okla, 2011.

To examine how project operations would affect instream flow conditions, including the amount of flow and water quality JHI will research published documents. Literature on how raising lake levels and fluctuation of lake levels can potentially impact Sweetheart Lake water quality will be researched and taken into account when developing operational plans during the construction and operational phases of the Project.

5.2.2 Study Component #2 – Sweetheart Creek Aquatic Survey assessment, evaluation, analysis and possible PM&E measures

Sweetheart Creek Bypass Study Area.

The Sweetheart Creek Bypass Reach includes the Sweetheart Creek areas not described in the anadromous reach and those below the immediate lake outlet. This area includes those determined to be above the lowest barrier to fish passage upstream to the Project dam location. . Based on initial scoping and consultation objectives in this area include:

• Identify all resident species and characterize life stage timing in the Bypass reach area.

• Inventory and map stream habitats and determine how habitat would be affected by changing flows, including the amount of flow and water quality.

• Evaluate Lower Sweetheart Lake outlet to determine if outmigrating aquatic life can return to the lake.

• Environmental and channel maintenance flows for the bypass reach should be identified and provisions developed to release these flows from the water reservoir. .

Method

To identify all resident species and characterize life stage timing in the Bypass reach area JHI will deploy minnow traps, hoop nets, cast nets and fly/cast rod surveys in locations above the barrier falls of the

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anadromous reach which are safe to gain access to. As mentioned in previous documents, there is not any current documentation to verify if the bypass reach supports resident fish, but seasonal attempts will be made to verify the presence/absence of resident fish. Given the terrain and stream gradients, sampling this reach could be extremely difficult if not impossible.

During these surveys JHI will diligently record all effort, and all capture data will include by specie, size, date, as well as photographs of the area around the point of capture. If presence is found, JHI will expend more effort to determine abundance with similar capture methods described in other sections. Also if presence is found, and will, through desk top study, characterize life stage timing.

To inventory and map stream habitats and determine how habitat would be affected by changing flows and examine how project operations would affect instream flow conditions, including the amount of flow and water quality JHI will use the following methods due to the geophysical constraints mentioned above. JHI will use desktop study, topography, and satellite photos (and foot surveys where applicable and safe) to identify channels and side streams of the bypass reach to assist in providing non-Lake stream flow estimations. JHI will analyze through photos how habitat will be affected by changing water flows. During surveys researchers will take water samples in the bypass reach to serve as a baseline for water quality in the bypass reach, and photograph and document any fish passage barriers.

Using the above environmental data, channel maintenance flows for the bypass reach will be researched and provisions considered.. JHI will incorporate into future water impoundment infrastructure analysis a possible bypass that will provide release of flows from the proposed Sweetheart Lake infrastructure at the outlet of Sweetheart Lake.

6.0 Water Quantity and Water Quality analysis and PM&E.

The overall water system study area consists of the Sweetheart Lake, Sweetheart Creek and tidelands of Gilbert Bay. More detailed site specific water quantity and quality analysis for the above areas is contained in their respective Aquatic Biological Survey sections above. Overall Water Quality and Quantity issues that were identified in SD2 are:

• Effects of project construction, operation, and maintenance on nutrients, erosion, sedimentation, and turbidity levels of Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay.

• Effects of project construction, operation, and maintenance on changes to nutrients,

water temperature, dissolved oxygen, dissolved gas levels, and rock leachate of Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay.

• Effects of contamination via accidental releases of fuels, lubricants, and other wastes

from construction equipment, machinery and operations on Lower Sweetheart Lake, Sweetheart Creek, and Gilbert Bay water quality.

• Effects of project construction and operation on Sweetheart Creek flows.

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Based on these SD2 issues, as well as scoping and consultation water quantity objectives in this area include:

• Perform hydrologic studies of seasonal streamflow in Sweetheart Creek and Lower Sweetheart Lake. These studies may be based on field data and combined with historical US Geological Service stream data and referenced with measured data in nearby basins.

• Examine and evaluate whether instream flow or lake level regimes adopted during

licensing would affect existing permanent and conditional water rights in the potentially-affected waters.

• Evaluate and document exact location of barrier falls and relationship for Alaska Fish and

Game water reservation for the anadromous reach of Sweetheart Creek. Like the water quantity objectives above, specific water quality objectives were identified and include:

• Examine the characterization of the temperature, dissolved oxygen, turbidity of waters affected by the project. Study will examine potential impact and mitigation of potential construction and operational effects on water quality. These water parameters are measured either continuously or periodically (seasonally, daily or weekly), using modern equipment capable of high accuracy and reliability. Water quality surveys will be conducted on Lower Sweetheart Lake.

• Review possible impacts on salt water marine life from changes in timing of freshwater

inputs to include ice formation into Gilbert Bay. As stated above site specific objectives are contained in the sections respective to their specific localized study area. Below are generalized methods pertaining to the overall issues and objectives identified in SD2. Method

In order to perform the above stated objectives JHI and its contractors will use either both site specific data obtained during this and previous studies as well as published literature where applicable. JHI and its contractors will perform desk top research and analysis of previous work previously completed by agencies in the project area for study components to serve as a reference and base line where applicable. This desktop research will be combined with data obtained during this study and analyzed with other applicable published studies and literature where it is deemed appropriate.

Hydrologic studies of seasonal stream flow in Sweetheart Creek and Lower Sweetheart Lake will be performed with stream gages and field data designed to acquire data at USGS standards. This information will be combined with historical US Geological Service stream data and referenced with measured data in nearby basins. JHI and contractors will then evaluate whether instream flow or lake level regimes will affect site specific issues and the ADFG water reservation application.

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Based on these analyses and evaluations it will then be determined on how best to serve mutual interests upon licensing and operation. JHI and contractors will determine and document exact location of barrier falls and its relationship to the Alaska Fish and Game water reservation for the anadromous reach of Sweetheart Creek. If this relationship is deemed different than the current ADFG listing (ADFG 2009) then JHI will work in coordination with the ADFG habitat division to amend the current listing. Utilizing scientific grade equipment, JHI and contractors will examine the temperature, dissolved oxygen, and turbidity of Sweetheart Lake. Also JHI will examine the potential impact and mitigation of potential construction and operational effects on water quality. JHI will monitor these issues during construction and operation and mitigate these effects using BMP’s or other appropriate means. JHI and contractors will review possible impacts on salt water marine life from changes in timing of freshwater inputs into Gilbert Bay including ice formation. This component of study will utilize historical and current stream flow data with proposed water flows and relate it to operational timing as it relates to a spectrum of economic and environmental issues. Based on this modeling, it will be determined if there are likely impacts or not on changing freshwater input timing into Gilbert Bay. This section of this component will be completed by contractor performing 4.2.2 Study Component #2 – Tidewater Resource assessment, evaluation, analysis and possible PM&E measures. Based on site specific issues, current guidelines and other applicable plans, recommendations will be suggested for development of a spill and containment plan for materials and substances used in development, construction and operations. Borrow pit containment recommendations will be developed if vicinity rock has harmful leachate qualities that are different from what naturally occurs in the environment. As with other issues listed above, JHI will monitor these issues during construction and operation and mitigate these effects using BMP’s or other appropriate means.

7.0 Agency Resource Management Goals

Aquatic resources including fish and their habitats are generally protected by a variety of state and federal mandates. In addition, various land management agencies, local jurisdictions, and non-governmental interest groups have specific goals related to their land management responsibilities or special interests. These goals are expressed in various statutes, plans, and directives: • Alaska Statute 41.14.170 provides the authority for state regulations to protect the spawning, rearing, or migration of anadromous fish. Alaska Statute 41.14.840 regulates the construction of fishways and dams. State regulations relating to fish resources are generally administered by ADFG. In addition to the state statutes, the following resource management plans and directives provide guidance and direction for protection of fish resources and aquatic habitats on lands within or adjacent to the Project area:

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• Magnuson-Stevens Fishery Conservation and Management Act (PL 104-267) provides federal protection to “those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.” NOAA’s National Marine Fishery Service (NOAA Fisheries) is responsible for designating Essential Fish Habitat (EFH). In the case of anadromous fish streams (principally salmon), NOAA Fisheries has designated the AWC prepared by ADFG (Johnson and Klein 2009) as the definition of EFH within freshwater habitats. • Aquatic Resources Implementation Plan for Alaska’s Comprehensive Wildlife Conservation Strategy, September 2006. Prepared by Alaska Dept. of Fish and Game, Div. of Sport Fish. • Our Wealth Maintained: A Strategy for Conserving Alaska’s Diverse Wildlife and Fish Resources. Prepared by Alaska Department of Fish and Game, Juneau, Alaska. xviii+824 pp. Management and land use plans relevant to Aquatic Resources Study Components:

• Juneau Coastal Management Plan. City and Borough of Juneau, Alaska Department of Natural Resources;

• Tongass Land Use Management Plan. United States Forest Service, Tongass National

Forest, Juneau. 2008;

• Juneau State Land Plan, Alaska Department of Natural Resources.

• City and Borough of Juneau, 2008 Comprehensive plan

8.0 Project Nexus The proposed Project may have potential impacts on aquatic resources within Sweetheart Creek and Lower Sweetheart Lake. The studies described above are intended to provide sufficient information regarding the nature of the existing aquatic resources such that these potential impacts can be adequately assessed. A discussion of the data will be presented in the study report, and will be used to inform the development of protection, mitigation, and enhancement measures to be proposed in the draft and final License Applications.

9.0 Consistency with Generally Accepted Practices

Sampling methodology for Sweetheart flats/Gilbert Bay, Sweetheart Creek, and Lower Sweetheart are designed in consultation with the public and resource agencies. Quality control of all study plans is maintained by using established methods used elsewhere to assess similar potential resource impacts and are reviewed by outside expert scientific reviewers. Methods proposed herein (use of observation surveys, minnow trapping, and angling) are generally-accepted practices for assessing fish resources. The instream flow approach, as a whole, is custom-designed for Sweetheart Creek and its unique hydrology, geomorphology, and fish resources. However, each component of the study is a well known and accepted technique for

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study application in the field. The integration of these components is accomplished through post-processing and analysis of results. Macroinvertebrates will be collected using the sampling method described by Eaton et al. (1998). Surber sampling is a preferred method of the USGS and ADFG. Periphyton will be collected using methods from Eaton et al. (1998).

9.1 Aquatic Resources Aquatic Resource Study Components will follow standard practices and generally accepted protocols established by the USFS, ADFG, and USFWS. Where applicable Aquatic Resource Study Components will follow standard USFS. 2001. Forest Service Handbook, FSH 2090.21. Aquatic Habitat Management Handbook. Alaska Region 10 amendment 2090.21-2001-1. 182 pp. Other standard accepted practices and protocols may be used after consultation with applicable agencies.

10.0 Schedule for Conducting the Study

REPORTING A draft Aquatic Resources Report documenting current 2012 data collection and analysis will be submitted for agency review as early in the winter of 2012 as possible, given the need to continue various field observations. The object is to provide sufficient review time for this subject prior to submission of the Project Draft License Application in 2012.

10.1 Anadromous and Tidewater Resource Study Schedule

4.2.1 Study Component #1 – Anadromous Resource assessment, evaluation, analysis and possible PM&E measures. Anadromous field studies will begin in early June in order to check for the presence of spring steelhead and ensure that the initial portion of the sockeye salmon is observed. Field surveys in this area will end in the late fall when it is concluded that in migration is complete.

4.2.2 Study Component #2 – Tidewater Resource assessment, evaluation, Analysis and possible PM&E measures .

Tidewater resource assessment will take place throughout 2012.

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10.2 Freshwater Resources Study Schedule

5.2.1 Study Component #1 – Sweetheart Lake and Inflow Tributaries Aquatic Survey assessment, evaluation, analysis and possible PM&E measures Resident Population spawn habitat Surveys.

Generally the Sweetheart Lake and Inflow Tributaries studies will begin after ice out which takes place in mid to late May and continue through the Dolly Varden spawning season in the fall (Table 4 ). Based on lake temperature isopleths (Yanusz and Barto 1994) the main body of Lower Sweetheart Lake warms to temperatures conducive to initiating spawning in Rainbow Trout in early to mid-June (Behnke 2002). Capture techniques will take place in the summer when trout spawning activities are complete and will end when char spawning begins in late summer early fall.

5.2.2 Study Component #2 – Sweetheart Creek Aquatic Survey assessment, evaluation, analysis and possible PM&E measures.

Studies in the Sweetheart Creek Bypass Reach will take place as conditions and time permit likely sometime in mid-summer (Table 4 ).

Table 4. Freshwater Resources Study Schedule.

Study Component Study Area Study Period

Sweetheart Lake and Inflow Tributaries Aquatic Survey Assessment

Sweetheart Lake Late May (ice out) to Early November

Inflow Tributaries Late May (ice out) to Early November

Sweetheart Creek Bypass Reach Aquatic Surveys Assessment

Bypass Reach Mid-Summer, as flows and conditions permit

6.0 Study Component – Water Quantity and Water Quality analysis and PM&E Water Quantity and Water Quality studies will be conducted in the 2011 and 2012 study seasons. 10.3 Field Logistics Food, lodging and transportation for the field crew will be supplied by the M/V Lizzy J, a fully contained vessel to be anchored in Gilbert Bay for periods requiring overnight stay for the duration of the 2012 survey, if necessary. In the absence of the M/V Lizzy J, another suitable

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vessel will be supplied. A vessel with power will be supplied for reconnaissance and field crew transportation in and around Gilbert Bay. At no time will trash or waste of any kind be emitted from the vessel. A small power skiff will be used on Lower Sweetheart Lake. A helicopter or float plane will be necessary to access survey areas on Lower Sweetheart Lake. Logistics and timing of surveys will be closely coordinated with JHI. Agency personnel and Tribal personnel may attend field visits upon approval of JHI, contractor and field logistic arrangements.

11.0 Provisions for Technical Review Opportunities for a review of draft study plans by agencies will be provided. All study plans and reports will be reviewed by JHI for subsequent distribution for review by agencies and interested parties.

10.1 Quality Control

All field work and data collection will be conducted by experienced personnel to professional industry standards by qualified team members. Senior and experienced professional staff will conduct pre-field work reviews of all study plan components. Consistency and completeness will be assured in all field procedures. Data will be recorded on custom standard datasheets; datasheets will be checked for accuracy and completeness by someone other than the recorder. Data entry and management will use Excel spreadsheets or other project-specific system for data management. JHI contractor will provide multiple level levels of QA/QC.

All field work will be performed to professional industry standards by qualified team members. Senior and experienced professional staff will conduct pre-field work reviews of all study plan components.

The technical reports will be in a form suitable to support development of Exhibit E of the License Application for the proposed Project. Draft reports, maps, and calculations will be reviewed by competent personnel approved by ADFG.

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12.0 References

Alaska Department of Fish and Game (ADFG). 2009a. Anadromous Waters Catalog, Nomination Submission Guidelines. ADFG Habitat and Restoration Division, Anchorage AK. http://www.sf.adfg.state.ak.us/SARR/AWC/index.cfm/FA/noms.guidelines ADFG, 2009b Catalog of waters Specified as Important for the Spawning, Rearing, or Migration of Anadromous Fishes. ADFG Habitat and Restoration Division, Anchorage AK. ADFG, 2009c. Atlas to the Catalog of Waters Specified as Important for the Spawning, Rearing, or Migration of Anadromous Fishes. ADFG Habitat and Restoration Division, Anchorage AK. Armstrong, R.H., 1984. Migration of Anadromous Dolly Varden Char in Southeastern Alaska-A Manager's Nightmare. p. 559-570. In L. Johnson and B.L. Burns (eds.) Biology of the Arctic Char, Proceedings of the International Symposium on Arctic Char. Winnipeg, Manitoba. May 1981. Univ. Manitoba Press, Winnipeg. Barbour M.T., J. Gerritsen, B.D. Snyder, and J.B. Stribling. 1999. Rapid bioassessment protocols for use in streams and wadable rivers: periphyton, benthic macroinvertebrates and fish. Second edition. EPA 841/B-99-002. U.S. Environmental Protection Agency, Office of Water. Washington D.C. (This document is available through libraries and on the web at www.epa.gov/owow/monitoring/rbp/.) Barbour, M.T., J. Gerritsen, B.D. Snyder, and J. B. Stribling. 1999. Rapid bioassessment protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates, and fish, Second Edition. EPA 841-B-99-002. U.S. Environmental Protection Agency; Office of Water; Washington, D.C. 326 pp. Behnke. R.J. 2002. Trout and salmon of North America. The Free Press, a division of Simon and Schuster, Inc. New York, NY. Bisson, P.A., J.L. Nielson, R.A. Palmason, and L.E. Grove. 1982. A system of naming habitat types in small streams with examples of habitat utilization by salmonids during low stream flow. Pages 62-73 in N.B. Armantrout, editor. 1981, Portland, Oregon, Western Division, American Fisheries Society. Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. In Influences of forest and rangeland management on salmonid fishes and their habitats. Edited by W.R. Meehan. American Fisheries Society Special Publication No. 19. Bethesda, Maryland. Pp 83 – 138. Bryant, M.D. 2002. Estimating fish populations by removal methods with minnow traps in Southeastern Alaska streams. North American Journal of Fisheries Management.

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Kershner, Jeffrey L.; Archer, Eric K.; Coles-Ritchie, Marc; Cowley, Ervin R.; Henderson, Richard C.; Kratz, Kim; Quimby, Charles M.; Turner, David L.; Ulmer, Linda C.; Vinson, Mark R. 2004. Guide to effective monitoring of aquatic and riparian resources. Gen. Tech. Rep. RMRS-GTR-121Fort Collins, CO: U.S. Department of Agriculture, Rocky Mountain Research Station. Klein, R. 1997. The effects of marinas and boating activities upon tidal waters. Community and Environmental Defense Services. Owings Mill, MD. 23 pp. Murphy, B.R., and D.W. Willis, editors. 1996. Fisheries techniques, 2nd edition. American Fisheries Society, Bethesda, Maryland. National Marine Fisheries Service. 2004. Essential Fish Habitat Consultation Guide. Office of Habitat Conservation. Silver Spring, Maryland Nordlund, Bryan. Designing fish screens for fish protection at water diversions. June 10, 1996. Portland, OR: National Marine Fisheries Service. Northcote, T.G. and D.W. Wilkie. 1963. Underwater census of stream fish populations. Transactions of the American Fisheries Society 92:146-151.

Powers, P. D. and J. F. Orsborn. 1985. Analysis of Barriers to Upstream Fish Migration - An Investigation of the Physical and Biological Conditions Affecting Fish Passage Success at Culverts and Waterfalls. Final Project Report Part 4 of 4. Report to Bonneville Power Administration. Albrook Hydraulics Laboratory, Washington State University, Pullman, Washington. Quinn, T.P. 2005. The behavior and ecology of Pacific salmon and trout. American Fisheries Society. Bethesda, MD. University of Washington Press. Seattle and London. Rosenberg, D. M. and V.H. Resh. 1993. Introduction to freshwater biomonitoring and benthic macroinvertebrates. Pages 1-9 in D.M. Rosenberg and V.H. Resh, editors. Freshwater biomonitoring and benthic macroinvertebrates. Chapman and Hall, New York. Round Butte Dam Selective Water Withdrawal, Design Basis Report, prepared by CH2M HILL Inc. for Portland General Electric and The Confederated Tribes of Warm Springs, 2007 Smith, A.K. 1973. Development and application of spawning velocity and depth criteria for Oregon salmonids. Transactions of the American Fisheries Society 102:312-316. Thompson, K. 1972. Determining stream flows for fish life. Pages 31-46 in Proceedings of Instream Flow Requirement Workshop, Pacific Northwest River Basins Commission, Portland, OR.

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Thurow, R.F. 1994. Underwater methods for study of salmonids in the Intermountain West. United States Forest Service, Intermountain Research Station, General Technical Report INT-GTR-307, Ogden, Utah. Wallace, J.B. and J.R. Webster. 1996. The role of macroinvertebrates in stream ecology function. Annual Review of Entomology 41:115-139. Watson, R. 1999. Salmon, trout and charr of the world. Swan Hill Press, UK. USFS. 2001. Forest Service Handbook, FSH 2090.21. Aquatic Habitat Management Handbook. Alaska Region 10 amendment 2090.21-2001-1. 182 pp. USFS. 2004. Guide to Effective Monitoring of Aquatic and Riparian Resources. General Technical Report RMRS-GTR-121. USFS.2010. Region 10 Channel Type User Guide. http://www.fs.fed.us/r10/tongass/forest_facts/ct_guide/index.shtml Yanusz, R. and D Barto. 1994. Draft sockeye salmon smolt production and emigration survival from the initial stocking of Sweetheart Lake. Unpublished Fishery Research Bulletin. ADFG Division of Commercial Fisheries Management and Development. Juneau, AK. 116 pp.

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Appendix A ADFG Sweetheart Lake 1953, 1954 Stocking Report

42

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Appendix B Agency Comment Table

Table. ADFG Sweetheart Lake Basin

Comment/Need Number

Comment Summary Response and Study Plan Location

ADFG 1 Document baseline population characteristics, seasonal movements, and seasonal habitat use for Dolly Varden and rainbow trout in Sweetheart Lake and its inlet and outlet streams.

JHI will use a combination visual observation methods and capture techniques in order to describe baseline population characteristics, and seasonal movement and habitat use of affected resident fish populations. Pp 28-29

ADFG 2 Identify important spawning habitats and spawn timing for resident rainbow trout and Dolly Varden.

JHI will use visual observation methods in order to document spawning areas and timing. Temperature information, visual observations, as well as fish condition (ripeness) during capture will be used to identify spawn timing. Probable and documented spawning areas will be analyzed using accepted substrate analysis techniques. PP 28-29

ADFG 3 Quantify and describe existing littoral zone and inlet stream habitats that would be inundated with the proposed increase in reservoir stage.

JHI will use existing information such as Aerial photography and USDA and USFWS sources to begin identifying habitats and will supplement this with onsite studies.pp28-29

ADFG 4 Assess the potential impacts of project-induced seasonal reservoir fluctuations on spawning and rearing habitats in inlet streams, including impacts on channel morphology and substrate conditions.

All documented and probable spawning areas will be marked by elevation and will be examined by substrate channel class, slope, and barriers. Following a literature review JHI will evaluate potential quality and quantity of available habitats during project operations. Pp28-29 according to low and high reservoir operations and high and low water years in order determine parameter s for flow regimes later

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ADFG 5 Assess the ability of fish to access inlet streams in relation to reservoir stage, particularly during spawning periods.

See ADFG 4

ADFG 6 Evaluate water temperatures in relation to reservoir stage

Data array logger

ADFG 7 Evaluate the potential for fish entrainment and impingement at the project intake. A fish screen system will most likely be required to prevent entrainment

JHI will evaluate the potential for fish entrainment and impingement. JHI will also review existing literature and fish screen designs (Norlund) as while taking into account features unique to the project in designing any fish screen designs. ( see Designing Fish Screens for Fish Protection at Water Diversions, National Marine Fisheries Service, Bryan Nordlund, June 10, 1996).

ADFG 8 Design and evaluate downstream passage facilities for sockeye smolt.

JHI proposes to install a site and species specific "smolt line" based on current designs. See page 10.

Comment/Need Number

Comment Summary Response and Study Plan Location

ADFG 9 Assess baseline relative abundance, distribution, and periodicity (seasonal use of habitat for spawning, incubation, rearing, and passage) by species and life stage.

JHI will use visual observation surveys in order to describe relative abundance, distribution (along with mapping), and periodicity by species and life stage See pp.*****22-23 currently

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ADFG 10 Inventory and map existing stream habitat.

Beginning with existing aerial photography JHI will use overlapping photographs to add detail and update stream maps as studies progress. These maps will be used during stream surveys to describe fish location and use. Pp22 currently

ADFG 11 Develop relations between seasonal instream flows, stream temperatures, and habitat quantity and quality (for spawning, incubation, rearing, and migration).

JHI I will use stream gage measurements as well as temperature and fish survey data gathered as studies progress to develop relations between instream flows stream temperatures and habitat quality and quantity for species and life stages present. Pp 23

ADFG 12 Evaluate the potential for false attraction of fish to the project tailrace and develop plans to mitigate.

JHI recognizes the potential for false attraction and is the process of developing plans to mitigate this effect through a tailrace spawning channel. Pp. 24

ADFG 13 Determine if ramping rates are needed for tailrace discharges.

Generally, if no site specific studies are conducted, ADFG recommends ramping rates to protect anadromous fishes that have been developed by the Washington Department of Fish and Wildlife (WDFW) (Hunter 1992)1

ADFG 14 Develop plans for protecting instream flows for fish during emergency and routine maintenance shutdowns of project operations.

JHI will identify bypass considerations to be incorporated in the project infrastructure design. See Pp. 23.

Table USFS All

Comment/Need Number

Comment Summary Response and Study Plan

Location

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USFS 1 . A study which documents population sizes, spawning times and spawning locations would be helpful in addressing potential impacts of the hydro plant on the fishery

See ADFG 1,2, 3, 4, 5,

USFS 2 Proper screening should be installed to prevent resident fish from entering the penstock and being transported through the turbines.

See ADFG 7

USFS 3 A thorough study should be conducted which documents population sizes and species of anadromous fish in Sweetheart Creek, as well as surveys of available spawning and rearing habitat, and continuous stream flow and stream temperature measurements.

SEE ADFG 9-14

Comment/Need Number

Comment Summary Response and Study Plan

Location

USFWS 1 Identify all resident and anadromous species and characterize life timing in the area

See ADFG 1,2,9

USFWS 2 Inventory and map stream habitats and determine how habitat would be affected by changing flows

See ADFG 3,4, ADFG 10, 11

USFWS 3 Identify potential fish passage barriers See ADFG 4,5

USFWS 4 Examine how project operations would affect instream flow conditions including water quality and quantity

See ADFG 11

USFWS 5 Evaluate ramping rates See ADFG 13

USFWS 6 Evaluate current resident spawning conditions and effect of project operations on resident spawning in Lower Sweetheart Lake Basin

See ADFG 2,4,5,6.