May 31, 2019 Chad Loflen Senior Environmental Scientist Regional Water Quality Control Board, San Diego 2375 Northside Drive, Suite 100 San Diego, CA 92108 Via Email: sandiego@waterboards.ca.gov Dear Mr. Loflen: Subject: Comment – Proposed Basin Plan Amendment to Incorporate Biological Objectives PIN: CW-825417 Attn: Chad Loflen The County of San Diego (County) appreciates the opportunity to provide comments on the Proposed Amendment to the Water Quality Control Plan for the San Diego Region to Establish Biological Water Quality Objectives for Perennial and Seasonal Streams (“Biological Objectives”). As one of the largest jurisdictions regulated under the San Diego Region Phase I Municipal Separate Storm Sewer System (MS4) Permit (Phase I MS4 Permit), the County is very interested in water quality regulations that are reasonable, founded upon sound science, and that move our region forward by improving water quality in a productive and responsible way. The County appreciates the San Diego Regional Water Quality Control Board’s (San Diego Water Board) willingness to meet with affected parties to consider alternative viewpoints on the proposed regulation prior to finalizing the Biological Objectives. The County recognizes the importance of the biological integrity of the county’s waterways and acknowledges the San Diego Water Board’s leadership in the Clean Water Act’s mission “to protect the physical, chemical and biological integrity” of waterways. To that end, the County is a supporting partner and participates in the Southern California Stormwater Monitoring Coalition’s Southern California Bioassessment Program. Further, the County was an active participant in the United States Environmental Protection Agency’s (USEPA’s) Causal Assessment Test Cases conducted at four locations in California that included a site in the San Diego River. The causal assessment tools developed by USEPA were given a “test drive” in California to identify potential causes of biological impairments and led to the development of the Causal Assessment Evaluation and Guidance for California document.

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The County’s comments in this letter come from the perspective of wanting to ensure that current and future stormwater management program efforts yield a corresponding return on investment, providing a meaningful benefit in terms of environmental health. To this end, the County supports the stated goal of the Biological Objectives project to “use biological assessment (‘bioassessment’) to better protect and restore waters by facilitating a broader evaluation of the effects of stressors that extends beyond the existing regulatory convention of analyzing for individual chemicals.” Additionally, the County supports the San Diego Water Board’s sentiment, as described in the Draft Staff Report, that using biological objectives instead of individual chemicals on a pollutant-by-pollutant basis will allow Total Maximum Daily Load (TMDL) assessments and implementation to be more effective and efficient and allow for regulated parties to consider more focused best management practices (BMPs) for their planned discharges. However, the County is concerned that the proposed Biological Objectives and associated implementation provisions as written will not effectively achieve these goals and may not result in directing resources to improving stream conditions. The primary concerns are:

1. The proposed Biological Objectives are inconsistent with, and do not incorporate lessons learned and information developed for, the Statewide Biointegrity Plan. In particular, the proposed objectives do not consider the information regarding challenges with attaining the objectives in developed landscapes, input from the Science Panel about the appropriate use of reference reach approaches, and concerns regarding the applicability of the objectives to intermittent waterbodies. In addition, setting a single threshold for impairment does not account for the natural variability expected for reference sites from year to year.

2. The majority of other states that have developed biological objectives have acknowledged the reality that not all waterbodies will be able to attain reference conditions and have therefore either not included numeric objectives or have set different numeric expectations for different waterbody types. Through the objective-setting process, the other states have demonstrated that utilizing different objectives can provide a better mechanism than single thresholds for improving waterbody condition, prioritizing actions, and conveying the benefit of waterbody improvement to the public.

3. Considering different expectations for different types of waterbodies is consistent with federal requirements for establishing water quality standards. The changes to the regulations governing establishment of USEPA water quality standards adopted in 2015 describe an approach that can be applied in the adoption of biointegrity objectives in the San Diego region that will yield consistency with both the Clean Water Act and the California Water Code (CWC). This approach aligns with the national goal described in Section 101(a)(2) of the Clean Water Act, which is “water quality that provides for the protection and propagation of fish, shellfish and wildlife and for recreation in and on the water, whenever attainable.”

4. Applying the proposed objectives to seasonal waterbodies creates significant challenges for sampling, identifying causes of lowered biological integrity, and determining the applicability of the objectives. These challenges need to be addressed before the objectives are applied to seasonal waterbodies.

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5. There are inconsistencies between the Basin Plan language, the Draft Staff Report, and the Draft Substitute Environmental Document (SED) regarding the compliance requirements for Phase I stormwater permittees. This lack of clarity in the Basin Plan language prevents a complete understanding of the compliance requirements for Phase I stormwater permittees and, thus, an evaluation of the potential impacts on the County. Furthermore, the proposed implementation provisions for Phase I stormwater permittees will result in immediate non-compliance challenges that are not adequately addressed by the provisions.

6. The proposed numeric compliance threshold is not tied to beneficial use protection, but to reference conditions, which may be better than the conditions required to meet beneficial uses. If the San Diego Water Board elects to use a reference approach to set an objective, then an analogous pool of reference sites should be used to reflect local environmental conditions.

7. The implementation approach as described is not likely to result in effective and efficient implementation. Much of the implementation approach relies on the ability to determine if dischargers are causing or contributing to lowered California Stream Condition Index (CSCI) scores and identifying the causes of the lowered scores. However, there are significant technical challenges with the available tools, and it may not be possible to make these findings. The objectives do not provide any mechanisms to address situations where the causes cannot be clearly identified. The County also has concerns that the tools are not sufficiently evolved to support implementation as proposed, which will create inconsistencies in implementation and wasted resources when sources of lowered biological integrity scores cannot be identified.

8. The proposed Biological Objectives project does not meet CWC Section 13241 requirements because it does not contain a sufficient analysis of the water quality that can be reasonably achieved through the coordinated control of all factors. Additionally, as demonstrated through the work conducted by the State Water Board, the proposed implementation program is unlikely to result in attainment of the objectives in many streams in the region. Additionally, the SED is deficient and has not adequately addressed impacts for each of the environmental topics.

9. Additional clarifications and responses to questions are requested to reconcile the numerous inconsistencies between the Basin Plan Amendment (BPA), Draft Staff Report and the SED that raise uncertainties about how the objectives will be implemented. Due to these uncertainties, the County is unclear of the possible impacts the Biological Objectives will have on County operations.

The issues identified above are discussed in more detail later in this letter. To address the County’s concerns, we support the proposal put forward by the California Stormwater Quality Association (CASQA) to first protect high quality streams and then adopt biological objectives for other waterbodies through a phased approach using the best science available and through a stakeholder-facilitated process. However, if the San Diego Water Board chooses not to adopt the CASQA recommendation, then the County requests consideration of a different phased approach based on the Antidegradation Alternative presented in the Alternatives Analysis section of the SED. The Antidegradation Alternative, with some proposed modifications, would consist of the following approach:

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1. The narrative objective and numeric compliance threshold would be applied to high

quality waters (reference waterbodies and other waterbodies that are currently meeting the proposed numeric compliance threshold).

2. The antidegradation approach would be applied to other waters during the first phase of objective implementation to ensure that degradation doesn’t occur while further studies are conducted to evaluate the need for objectives or numeric compliance thresholds for these waterbodies.

3. The first phase of implementation would only include perennial waterbodies with the proposed biological objective of a 0.69 CSCI score, which reflects the 10th percentile of reference stream sites in southern California, until challenges with identification and implementation of the objectives in seasonal waterbodies are addressed.

4. The biological objective would not apply to highly modified and engineered streams until additional research can be conducted to evaluate the potential effects of harm to life and property from flood waters and to evaluate the best attainable biological conditions.

5. For streams to which the antidegradation approach is applied, the implementation approach would include a process for evaluating the potential for improving stream condition and associated implementation actions that would result from those evaluations to encourage stream improvement. This process would address the concerns with the Antidegradation Approach outlined in the Alternatives Analysis in Section 1.8 of the SED.

The County would like to work with the San Diego Water Board and other interested stakeholders to develop the phased alternative approach through a facilitated process. By working through a facilitated process, the County is confident an alternative approach can be identified for seasonal streams and constrained or engineered channels that will achieve the San Diego Water Board Project goals and address the County’s concerns. The County has identified a number of significant concerns with the proposed objectives, primarily related to the application of the objectives to streams that are not high quality/reference streams. All of the concerns identified in this section could be addressed through the modifications to the proposed objectives outlined above. The following sections provide more detailed discussion of the County’s concerns.

1. Proposed Biological Objectives are Inconsistent with and do not Incorporate Lessons Learned and Information Developed for the Statewide Biointegrity Plan Development

The Statewide Biointegrity Plan development evolved over the course of several years as the State Water Resources Control Board (State Water Board) carefully evaluated available science, policy and implementation options. At the beginning of the process in 2010, the State Water Board was considering developing a numeric objective using a similar approach to that proposed by the San Diego Water Board. However, after input from the Science Panel, the CEQA Scoping meeting, and State Water Board management, the approach was modified in 2014 to a bioassessment framework with the possibility for a narrative objective that focuses on protecting high quality waters and assessing biointegrity statewide. Some of

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the factors that resulted in the change were summarized in a presentation to the Stakeholder and Regulatory Advisory Groups on October 12, 2011. The implementation issues identified included:

Identification of monitoring requirements

Identification of methods for determining thresholds (e.g. based on statistical benchmarks, acceptable species loss, combination of multiple metrics)

Determination of if the policy should be applied to modified streams and if exceptions for these waterbodies are included, how would the exceptions be developed

Determination of how and when causal assessments would be done and how situations where the causal assessments are inconclusive would be addressed

Identification of how waterbodies would be listed as impaired and the scale at which the listing would apply based on the monitoring data

Identification of when and how restoration would be required

Definition of how the objectives would be applied, including definitions for perennial and wadeable and the scale that a site assessment represents (e.g. site, reach size, watershed)

Additionally, as part of the CEQA scoping meeting, the State Water Board identified that establishing biological objectives based on reference conditions is unrealistic for many highly modified streams and in the May 18, 2011 Stakeholder Advisory Committee Meeting, the State Water Board identified that numerous sources of variability need to be evaluated in determining the potential objectives. Sources of uncertainty include the method, spatial and temporal application of the results, and the threshold derivation. As a result of the identified implementation issues noted above, at the Biological Objectives Stakeholder Advisory Group Meeting Summary May 24, 2012, “There was strong support for a phased approach to policy development and implementation.” In response to the numerous implementation issues, the State Water Board also began development of tools, definitions and resources to support the development of the Plan. In a January 15, 2015 presentation to the Biological Integrity Policy Stakeholder Advisory Group, the State Water Board provided a recap of the status of the Biological Integrity Plan development. The presentation included an overview of the policy framework developed in 2014 which includes:

Policy goals, including the following elements: o Identify streams or stream reaches in which biological condition is similar to

that in appropriate reference sites and prevent degradation inasmuch as it is within the State’s authority to do so.

o Identify streams or stream reaches in which biological condition is significantly different from appropriate reference condition and use this information to determine whether additional information is needed and to prioritize actions necessary to improve biological condition as appropriate.

Definitions, including a definition of a “sample-able stream” and “index period” to help standardize sampling and minimize variation in biological communities being sampled.

Expectations that the CSCI would be updated regularly to incorporate new data.

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Definition of the spatial extent to which a CSCI score would apply.

Methods for establishing current biological condition, including the use of a sensitivity analysis to determine the number of samples needed to detect a change in CSCI scores.

Identification of criteria for prioritizing where further investigation or causal assessments are needed.

Guidance for implementation in water quality control programs, including assessing trends in condition, measuring the effectiveness of management plan implementation, evaluating whether additional management actions are needed to improve conditions, and prioritizing areas that need management actions.

It is unclear how the San Diego Water Board addressed the implementation issues identified above that led to the State Water Board moving away from the development of a numeric biological objective based on a percentile of reference. It is also unclear how the policy framework, tools and definitions that were developed for the draft policy framework were considered and why deviations were made from that framework. In particular, it is unclear how the San Diego Water Board can use the same bioassessment database as the State and reach a conclusion that development of a single numeric threshold for all waters is appropriate when it is clear that attainment of those objectives is unrealistic for highly modified waterbodies. Three key elements of the State’s Biostimulatory/Biointegrity Plan support an alternative approach and should be carefully considered by the San Diego Water Board in developing the proposed objective: (1) possible consideration of different thresholds/expectations for constrained channels, (2) challenges expressed with selecting a single numeric threshold based on statistical distributions of reference data and (3) questions and uncertainty about the applicability of thresholds and tools to seasonal (intermittent) streams.

1.1 Consideration of Different Expectations for Constrained Channels

The State’s Biointegrity Plan recognizes that different biological expectations should be considered given the range of stream types possible (e.g., perennial, non-perennial, hardened channel, maintained natural channel, hydrologically modified, natural hydrology). As a result, the State’s plan includes a project called Predicting Biological Integrity of Streams Across a Gradient of Development in California Landscapes, or the “Developed Landscapes Project”. This project involved modeling to predict which CSCI scores are possible in a waterbody given a range of potential constraints represented by Geographic Information System (GIS)-based land use characteristics (accessed from the STREAMCAT database). One purpose of the project was to provide information to support “protecting biological integrity in streams by informing appropriate expectations or by prioritizing sites long and short term restoration activities.”1 The Developed Landscapes Project produced a modeling tool that can be used, among other things, to: (1) identify the stream segments in a region that are unlikely to obtain reference level CSCI scores owing to development, and (2) predict expectations for CSCI and ASCI scores (as a range of likely scores) for streams that fall into this category. Anthropogenic and natural landscape features that can constrain biological condition (such as impervious surfaces, non-native vegetation cover, road density and

1 Predicting Biological Integrity of Streams Across a Gradient of Development in California Landscapes Work Plan. SCCWRP,

CDFW.

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crossings, elevation, and geology) were used to create categories. The model can predict the range of CSCI scores that are likely for given sites and can also predict the probability of achieving a particular CSCI score. Although any CSCI value could be used to produce model output, a CSCI score of 0.79 (corresponding to the 10th percentile value for reference sites in Mazor et al. 20162) was used in model trials in 2017 to bin stream sites (with sufficient data) in California into three categories:

Likely high scoring (sites with <10% chance of scoring below 0.79)

Likely constrained (sites with <10% chance of scoring above 0.79)

Other (sites not in the upper two bins, but whose predicted score range includes 0.79)

This approach distinguishes settings where permanent or semi-permanent landscape features related to legal development combine to constrain biological condition independently of water quality and, thus, where management measures focusing on water quality are less likely to improve biological integrity. The Science Panel recommended improvements to the model to allow differentiation of constraints resulting from different types of stressors. This would allow a more refined consideration of the potential for restoration. Based on an assessment conducted of the available data in San Diego County from the SMC program and permit compliance monitoring, 66% of assessed samples would not meet objectives. Streams not meeting the objectives are often in channels where the Developed Landscapes Project tool indicates constraints exist that may not make attaining the objective feasible as shown in Figure 1. Given that land use constraints and modified streams in highly urbanized settings limit the biological and restoration potential of streams (red channels in the figure), prioritizing resources to protect the high quality streams (dark blue) and restoring streams that are more likely to improve (light blue) would likely lead to better environmental outcomes. Constrained streams (red channels) could be compared to other constrained streams to evaluate restoration potential.

2 Mazor, R. et al., 2016. Bioassessment in complex environments: designing an index for consistent meaning in different

settings. Freshwater Science 35(1):249-271.

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Figure 1. Comparison of CSCI scores from SMC and NPDES monitoring to Developed Landscapes Model Output3

3 GIS files from: ftp://ftp.sccwrp.org/pub/download/TMP/RaphaelMazor/Shapefiles.zip. With updated model data from Raphael

Mazor dated Dec 2017

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As part of the Statewide Biointegrity Plan development, the State Water Board identified two potential methods for addressing modified channels:

Exceptions to compliance with the water quality objective would be granted based on findings from site- specific use attainability analyses.

For streams that would not reasonably be expected to achieve “good” biological condition targets, the Water Boards may establish targets based on “best attainable.”4

The April 2017 Science Panel Report and the March 2019 review of the Channels and Developed Landscapes Manuscript both supported consideration of different thresholds for constrained channels. The Science Panel members highlighted the benefits of considering different thresholds or approaches for different types of waterbodies, including more cost-effective and productive management approaches and the value in considering likely biological condition in developing and evaluating management options. “Restoring a stream in poor condition when its surrounded by other streams in poor condition is unlikely to be as successful as restoring a stream in poor condition that is surrounded by streams in better condition.”5 The Science Panel also noted the value in considering different thresholds when setting goals for protection and management of waterbodies as follows:

“As acknowledged in the document, water resource managers need a way of estimating the degree to which individual waterbodies can support or achieve biological integrity goals. Specifically, we need objective ways of identifying waterbodies that are constrained in achieving biological integrity by historical land use and waterway alteration. This knowledge can then be used by policy makers to set practical goals for the protection or restoration of individual waterbodies and to prioritize management actions across waterbodies.”6

Recommendation: Consideration of the “best attainable” value of a constrained channel will result in the efficient and effective use of resources to reach appropriate restoration goals. The “best attainable” value could be established through the phased approach as summarized earlier in this letter.

4 Using Biological Assessment Tools for Regulating California Streams, Stakeholder Advisory Group Meeting, June 5, 2013

presented by Karen Larsen, Director Office of Information Management & Analysis, State Water Board. 5 Wadeable Streams Nutrient Objectives Science Panel Report Cliff Dahm, Charles Hawkins, Paul Stacey, Ken Reckhow, R. Jan

Stevenson, Lester Yuan Meeting: April 19-20, 2017. 6 Science Panel Report on Prioritizing Management Goals for Stream Biological Integrity Within the Developed Landscape

Context, March 2019.

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1.2 Selecting a Single Numeric Threshold does not Effectively Represent Beneficial Use Protection or Account for Natural Variability in Reference Waterbodies

The 10th percentile threshold used for assessing compliance does not reflect that a range of CSCI scores can be protective of a beneficial use condition. This same concern applies to other metrics (e.g. Algal Stream Condition Index “ASCI”) that are based on a percentile of reference. As part of the State’s Biointegrity Plan development, biological conditions are being related to CSCI and ASCI scores in the project entitled “Expert Interpretation of the Biological Condition Gradient in California Wadeable Streams”, or the “BCG Project”. The BCG Project used a panel of experts to sort California stream sites into narrative biological condition “bins” based on their biological communities – without being biased by information about “stressors.” The BCG Project’s expert panel evaluated data from several hundred bioassessment sites, and assigned them to one of six biological condition bins:

Bin #1: Natural structural, functional, and taxonomic integrity is preserved. Bin #2: Structure and function similar to natural community, with some additional taxa &

biomass; ecosystem level functions are fully maintained. Bin #3: Evident changes in structure due to loss of some rarer native taxa; shifts in relative

abundance; ecosystem level functions fully maintained. Bin #4: Moderate changes in structure due to replacement of some sensitive ubiquitous

taxa by more tolerant taxa; ecosystem functions largely maintained. Bin #5: Sensitive taxa markedly diminished; conspicuously unbalanced distribution of

major taxonomic groups; ecosystem function shows reduced complexity & redundancy.

Bin #6: Extreme changes in structure and ecosystem function. The results of this project revealed that sites that share particular CSCI scores may fall into any one of a number of biological condition bins. For example, sites with a score of 0.79 landed in one of four condition “bins” (bins 2-5) and had about an equal chance (near 40%) of being assigned to either Bin #3 or Bin #4. A wide range of scores (each with a probability distribution) was associated with each “condition” as shown in Figure 2.

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Figure 2. Proportional Odds Model depicting range of CSCI scores for BCG bins, taken from SCCWRP‘s July 5th, 2017 BCG Webinar

A CSCI score of 0.79 is associated with the 10th percentile of statewide reference sites in Mazor et al. (2015)7. In the illustration, we see that sites with a score of 0.79 (marked by the middle blue line) landed in one of four condition “bins” (bins 2-5). Following the descriptions of the biological condition bins below, it could be argued that many sites with scores of 0.79 and below (see range of purple and green data points in diagram) are systems in which ecosystem functions are largely intact. Rather than use a percentile of unaltered analogous streams from the reference pool distribution to define a bright-line CSCI threshold of impairment, the State’s Biointegrity Plan is evaluating ranges associated with these different biological condition bins developed using the Biological Condition Gradient (BCG) model. The analyses indicate that a CSCI threshold, such as the 10th percentile of reference (0.79), should not be construed as a bright-line to determine impairment. The analysis demonstrated that sites considered as meeting the same narrative standard of structure and ecological function, could span a wide range of CSCI scores. In summary, the BCG outcomes illustrate that setting ranges of CSCI for the assessment framework is more appropriate than single percentile values. Additionally, the Science Advisory Panel has consistently emphasized the natural variability in reference conditions and the need to consider that variability in determining reference conditions. As noted in the overview of the Science Advisory Panel’s findings and recommendations presented in the Stakeholder Advisory Group Meeting Summary from May 18, 2011 “no site is a perfect duplicate of other sites, and conditions at individual sites are also likely to vary over time. Reference condition is thus not a single number, but encompasses a range of condition(s) and the assessment tools are being developed to

7 Mazor et. al. 2015, The California Stream Condition Index (CSCI): A New Statewide Biological Scoring Tool for Assessing

the Health of Freshwater Streams, SWAMP Technical Memorandum, SWAMP-TM-2015-0002, September 2015, page 259.

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account for that.” The April 2017 Science Advisory Panel Report supports the concerns with selecting a single numeric threshold based on a statistical distribution of reference condition data as an objective. A comprehensive discussion of the challenges with this approach is included on pages 5 through 8 of the report. One of the key concerns with selecting a single reference value is that it does not account for natural variability and the relationship to biological condition is not explicitly explained as expressed below:

“However, the lack of both a rigorous justification for the selected threshold values (which logically implied that 10 or 25% of reference sites would be flagged as being in non-reference condition) and an intuitively clear biological interpretation of index scores were often confusing to scientists and stakeholders alike. Moreover, this approach did not couch the reference condition concept in context of the range of variation expected at individual waterbodies.”8

Recommendation: The Science Panel recommended against using the Reference Approach proposed for use in this Biological Objectives project as a mechanism for setting single numeric thresholds for the Statewide Biostimulatory/Biointegrity Plan. Instead, consider developing a range of expectations or method for accounting for variability using a phased approach as summarized earlier in this letter.

2. Most Other States That Have Developed Biological Objectives Have Used Tiered Approaches or Incorporated Considerations for Different Types of Waterbodies

The Draft Staff Report cites Ohio and North Carolina as examples of states that have adopted various approaches of biological criteria. According to the USEPA’s Bioassessment and Biological Criteria Website9, nineteen states have narrative objectives with numeric guidance and only five states have numeric objectives for biological integrity. Of the five states that have numeric objectives, all five have tiered classifications of waterbodies and four of the five set different objectives based on the different waterbody classes. Additionally, the concept of determining a “best achievable” condition for an urbanized stream is included in the objectives for several states and internationally, such as in Australia. The following state-by-state examples illustrate how the alternative state approaches protect high quality waterbodies and restore waterbodies, while recognizing hydrologic and temporal differences:

2.1 Maine

The Maine Department of Environmental Protection (MDEP) uses aquatic life use designations based on multiple thresholds and use categories. Waterbodies are classified from Class AA, the highest quality water systems, to Class C, waterbodies meeting interim Clean Water Act (CWA) goals while being impacted by human activities. The Biological Condition Gradient (BCG) was used by the MDEP to develop the narrative and numeric approaches for waterbody classifications. This approach was developed with the goal of protecting, maintaining, and restoring high quality aquatic biological conditions while

8 Wadeable Streams Nutrient Objectives Science Panel Report Cliff Dahm Charles Hawkins Paul Stacey Ken Reckhow R. Jan

Stevenson Lester Yuan Meeting: April 19-20, 2017, page 5 9 https://www.epa.gov/wqc/information-bioassessment-and-biocriteria-programs-streams-and-wadeable-rivers

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improving waterbodies to meet regulatory goals. The classification system is dynamic and intended to change over time as stream conditions improve. As stream conditions improve, a waterbody can move from Class C to Class B and so forth, demonstrating that the tiered aquatic life use approach does not create an artificial biointegrity ceiling placed on a waterbody. As seen in Table 1, between 1987 and 2012, waterbodies in Maine saw increases in Class AA and Class A designations, marking significant biological integrity improvements especially from previously designated Class B and Class C waterbodies10. This spectrum of biological integrity improvement is notably missing from the single threshold approach. Table 1. Improvements in Maine’s Waterbody Classifications from 1987 to 2012

MDEP also notes that there are significant management benefits to this approach which:

“offer[s] a broader range of management options to ensure that resource goals and objectives are neither underprotective of existing high-quality resources, nor needlessly burdensome for waters that may be permissibly affected by pressures from allowed human activities.”10

As significant financial investments are often needed to restore waterbodies, classifications help regulatory agencies and permittees communicate to the public the value of protecting high quality waters while enhancing public understanding of existing problems and restorable biocriteria targets. As Maine has learned from several decades of implementing biological objectives, “the pass–fail management paradigm, used by so many states, deprives the public of the more precisely resolved gradient of classification options that would allow them meaningful participation in local and statewide water resource planning (emphasis added).”10

Maine aquatic life objectives did not originally include the different tiers of thresholds and beneficial uses. The use classification system was overhauled during the development of the biological criteria because “The original use classification law contained unrealistically restrictive aquatic life standards that were undifferentiated by water quality class and were, therefore, unenforceable (emphasis added).”11

10 Davies, S.P., F. Drummond, D.L. Courtemanch, L. Tsomides, and T.J. Danielson. 2016. Biological water quality standards to

achieve biological condition goals in Maine rivers and streams: Science and policy. Maine Agricultural and Forest Experiment

Station Technical Bulletin 208. 11 Biological Criteria: State Development and Implementation Efforts, July 1991. USEPA Office of Water, EPA-440/5-91-003.

Mr. Loflen May 31, 2019 Page 14 of 37 2.2 Ohio

The Ohio Environmental Protection Agency (OHEPA) water quality standard for biological criteria includes a narrative statement with numeric objectives. The approach taken by the OHEPA emphasizes the protection of high quality waterbodies, by utilizing tiered aquatic life uses that ranges from “exceptional warmwater habitat”, with a higher biocriteria standard to meet, to “modified warmwater habitat”, with a lower biocriteria standard. The modified warmwater habitat use designation was based on the reference site data of physically altered streams and rivers that cannot fully attain the highest level of the biocriteria standard due to long-term and essentially irreversible physical macro-habitat modifications. The decision to use tiered aquatic life uses by OHEPA was based on scientific guidance that recognized that “attainable biological community structure and function is influenced by such widespread activities as intensive land uses, natural stream channel alterations (e.g. channelization), human settlement, roads and highways, and general land use conversion (e.g. deforestation) to suit socioeconomic desires.” 12 OHEPA additionally recognized that the “least impacted” conditions are not intended to represent pristine wilderness or pre-Columbian conditions. The biocriteria, as initially established, was intended to set a baseline expectation for biological integrity. While biocriteria have been established to reflect what can reasonably be attained given the background conditions, biocriteria can be recalculated as the biological integrity of modified stream systems improves over time.

2.3 North Carolina

The North Carolina Department of Environmental Quality uses a narrative biological criterion, with quantitative implementation translators for determining which waterbodies are attaining aquatic life uses. The narrative criterion states that “Waters shall be suitable for aquatic life propagation and maintenance of biological integrity.”13 To assess biological integrity for benthic macroinvertebrates, a bioclassifications approach is used, which contains five classifications for streams (Excellent, Good, Good-Fair, Fair, Poor) and three classifications for swamps (Natural, Moderate, Severe). To determine a bioclassification for a stream site, biotic index (BI) values are considered within the context of several factors such as stream size, flow regime, season of collection, and sample method.14 The Excellent bioclassifications is used as supporting evidence to designate the waterbody as either an Outstanding Resource Waters and High Quality Waters, which offers more protective guidelines. Waters with bioclassifications listed as Poor, Fair, or Severe are determined to be exceeding the narrative criterion and are placed in the Clean Water Act 303(d) List Category 4 or 5.15 As with the approaches previously discussed, the bioclassification approach prioritizes the protection of high quality waters and promotes improved biological integrity in streams through the restoration of degraded waters.

As shown in these examples, improvement in biological condition is supported when tiered approaches are used and setting different expectations for different waterbody types does not prevent improvements in waterbody conditions. Using a tiered approach allows better

12 Biological Criteria for the Protection of Aquatic Life: Volume II: User’s Manual for Biological Field Assessment of Ohio

Surface Waters, State of Ohio Environmental Protection Agency. 13 15A NCAC 02B .0211 Fresh Surface Water Quality Standards for Class Waters 14 Standard Operating Procedures for the Collection and Analysis of Benthic Macroinvertebrates (Version 5), North Carolina

Department of Environmental Quality, Biological Assessment Branch, February 2016 15 2014 Water Quality Assessment Process, North Carolina Division of Water Quality.

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prioritization of actions to advance biological integrity in an efficient and cost-effective manner. Recommendation: The County requests that the San Diego Water Board adopt an approach that considers multiple thresholds for different waterbody classes that reflect what can reasonably be attained given the background conditions. A facilitated process as discussed earlier in the letter could be implemented to develop Biological Objectives for different classes of waterbodies in a phased approach.

3. Considering Different Expectations for Different Types of Waterbodies is Consistent with Federal Requirements for Establishing Water Quality Standards

The changes to USEPA water quality standards regulations adopted in 2015 describe an approach that can be applied in the adoption of biointegrity objectives in the San Diego region that will yield consistency with both the Clean Water Act and the CWC. This approach aligns with the national goal described in Section 101(a)(2) of the Clean Water Act, which is “water quality that provides for the protection and propagation of fish, shellfish and wildlife and for recreation in and on the water, whenever attainable. (emphasis added)” The approach described in the Federal Register notice for the 2015 regulations is first to determine whether the desired aquatic life uses can be attained. USEPA recommends the consideration of the six factors described in 40 CFR 131.10 (g) in the determination of attainability. Those six factors are:

1. Naturally occurring pollutant concentrations prevent the attainment of the use; or 2. Natural, ephemeral, intermittent or low-flow conditions or water levels prevent the

attainment of the use, unless these conditions can be compensated for by a sufficient volume of effluent discharge without violating state conservation requirements to enable uses to be met; or

3. Human-caused conditions or sources of pollution prevent the attainment of the use and cannot be remedied, or would cause more environmental damage to correct than to leave in place; or

4. Dams, diversions, or other types of hydrologic modifications preclude the attainment of the use, and it is not feasible to restore the waterbody to its original condition or to operate such modification in a way that would result in the attainment of the use; or

5. Physical conditions related to the natural features of the water body preclude attainment of aquatic life protection uses; or

6. Controls more stringent than those requires by Sections 301(b) and 306 of the Act would result in substantial and widespread economic and social impact.

For waters that cannot meet the desired condition (i.e., in this case, waters that are not able to achieve a CSCI score of 0.79), USEPA recommends the establishment of different beneficial use descriptions and categories which reflect the highest attainable use for the category of water body (or the specific water body) in question. In developing information to support the evaluation of use attainability, USEPA recommends: (a) the identification of current and expected conditions of the water body, (b) the evaluation of the effectiveness of best management practices, including treatment options, and (c) the use of water quality models, load calculations, and other predictive tools. In discussing the highest attainable

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uses in water bodies, USEPA describes such uses as those that are attained when the most protective, attainable criteria are achieved. Examples of sub-categorical use designations that have been approved by USEPA include:

Limited warm water aquatic life use

Effluent dependent waters

Effluent dependent fisheries

Effluent dependent non-fish bearing waters

In each of these cases, it was determined that it would not be feasible for these waters to attain the same aquatic life assemblage that was expected of waters assigned the full aquatic life beneficial use designation. Many of the waterbodies in San Diego County contained engineered modifications prior to the establishment of the beneficial uses in the first San Diego Region Basin Plan. The aquatic life beneficial uses (e.g. WARM, COLD, etc.) were assigned to these waterbodies based on the aquatic communities that were present in the waterbodies at the time the Basin Plan was established. The definitions of the beneficial uses are broad and encompass the range of aquatic communities that can be present in different types of waterbodies because they were established by the State Water Board. While the Basin Plan did not specifically identify different beneficial use categories for different types of waterbodies, waterbodies with existing channel modifications were designated as having the aquatic life beneficial uses based on the aquatic communities present in the waterbody at the time, not reference condition communities. Establishing biological objectives that require waterbodies to attain conditions that were not present at the time the beneficial use was originally designated is inappropriate and should not be required. Recommendation: The County requests that the San Diego Water Board develop information to address the attainability of the proposed water quality objective and associated beneficial uses in a manner that is consistent with USEPA water quality standards regulations and CWC requirements. Additionally, the Chapter 4 BPA should clearly allow for the development of Use Attainability Analyses (UAAs) and site-specific objectives, in accordance with USEPA regulations and CWC requirements for those waters that cannot attain the proposed Biological Objectives. Additionally, the County requests that waterbodies with channel modifications that existing prior to the establishment of the first Basin Plan in 1975 be exempted from attaining the Proposed Biological Objectives. Overall Recommendation to Address All of Above Comments (Phased Approach): Modify the proposed Basin Plan Objective as follows:

1. Apply the narrative guidance and numeric compliance threshold to high quality waters (reference waterbodies and other waterbodies that are currently meeting the proposed numeric compliance threshold).

2. Use an antidegradation approach for all other waters to ensure that further degradation does not occur while further studies are conducted to evaluate the

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need for objectives or numeric compliance thresholds for these waterbodies in a future phase.

3. For waterbodies to which the antidegradation approach is applied, the implementation approach would include a process for evaluating the potential for improving waterbody condition and associated implementation actions that would result from those evaluations to encourage waterbody improvement.

4. Exclude Seasonal Streams from COVERAGE by the objectives

The narrative biological guidance in the San Diego Region will be applicable to all surface waters. However, as set forth in this policy, numeric biological objectives would only apply to perennial and seasonal streams. The Basin Plan Amendment defines seasonal streams as “any freshwater stream that is expected to be inundated with flowing water for at least four weeks between the months of February and October, except during periods of atypical or extreme drought….Seasonal streams do not include those streams that only exhibit ephemeral flow, which is flow that occurs only during or immediately following (e.g. 24-48 hours) rainfall events”. From a practical perspective, it is extremely difficult to definitively classify streams into one stream type given the gradient of possible flow regimes and year-to-year variability. It is problematic from a policy perspective to not know if a required objective applies to an individual seasonal stream. More guidance is needed for seasonal streams that may have variable year-to-year flow periods, and when a stream might be excluded for lack of adequate period of flow for a robust invertebrate community to develop. The Draft Staff Report addresses stream habitats that are acceptable for sampling (Section 4.5); however, the flow duration of many streams is not known, The proposed biological objective does not adequately address benthic macroinvertebrate community changes near the end of their flow cycle, and in fact, seems to indicate in Figure 15 of the Draft Staff Report that reduced flow at the end of a drying cycle does lower the CSCI score.

A high proportion of streams in the San Diego region are considered seasonal according to the definition given. A study published by SCCWRP (Mazor et al., 201216) identified 73% of streams in the San Diego region as being seasonal. The study also stated that these stream types support benthic macroinvertebrate communities that are distinct from those found in perennial streams, and that multi-metric indices designed to assess the health of benthic macroinvertebrate community were applicable to these stream types, as long as they flow long enough for the establishment of all benthic communities. It has been documented by Mazor et al. (2014) and others, that biologic metric scores can remain relatively steady in seasonal streams across a season. However, as was pointed out in Section 4.7.1 of the Draft Staff Report, they become much more variable and can decline quickly as the stream reaches the end of its drying cycle, particularly in moderate and high stressed non-perennial sites, which are more common in developed areas where the majority of bioassessment sampling for permit compliance takes place. The point on the hydrologic cycle from beginning of flow to drying is typically not known during a field bioassessment, and historic site reconnaissance has shown that streams often cease to flow more quickly than anticipated.

While it is clear that a representative and accurate CSCI score can be derived from a seasonal stream during some portions of its flow duration, it has not been demonstrated that this is also

16 Mazor, R., K. Schiff, P. Ode, and E.D. Stein. 2012. Final Report on Bioassessment in Nonperennial Streams. Report to the

State Water Resources Control Board. SCCWRP Technical Report 695.

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true as a seasonal stream nears the end of its flow cycle. Sampling a stream near the end of its flow may lead to improper evaluations of compliance or impairment based on inaccurate CSCI scores not representative of a seasonal stream’s true biological potential.

During the December 2018 Science Panel meetings, stakeholders raised concerns about the applicability of the science being developed for the Statewide Biostimulatory/Biointegrity Plan to intermittent or seasonal streams. The Science Panel agreed that while the CSCI was likely applicable to seasonal streams if they could be sampled during the appropriate period, the way in which the scores should be interpreted and applied in the policy context was not sufficiently vetted or explained. The Science Panel requested additional information on the applicability of the science and tools along the continuum of perennial to intermittent streams and more clarity on interpreting CSCI scores along this continuum. Recommendation: Only apply the objectives to perennial streams during the first phase of objective development. Use results from the Statewide Biointegrity/Biostimulatory Plan to determine applicability and appropriate interpretation of scores from seasonal streams during a future phase.

5. Address Inconsistencies and Clarify Compliance Requirements for Permit Dischargers

While the County supports the goals of the proposed Stream Biological Objectives, we have noted a few important omissions or inconsistencies between the proposed BPA, Draft Staff Report, and SED that make it difficult to clearly understand the overarching compliance requirements for MS4 dischargers. The process for assessing compliance is primarily based on whether discharges are “causing or contributing” to an exceedance of the biological objective. However, there are several steps in the process that are not fully clear, and the BPA language differs somewhat from the Draft Staff Report language. Figure 2 from the Draft Staff Report provides the best overview of the process, as applicable to all permittees. However, the information provided does not fully explain how the objectives will be implemented and the responsibilities of the various dischargers. As part of the Statewide Biological Objective Policy development, the State Water Board developed a comprehensive policy framework diagram and associated diagram of implementation requirements for various permit conditions. A similar overarching framework flow chart should be included in the Chapter 4 BPA to help address the comments provided in this section. The example framework flow chart from the Statewide Biological Objective Policy development is included as an attachment.

5.1 Cause or Contribute

Both the Draft Staff Report and the SED indicate that compliance is not based on an exceedance of the Stream Biological Objective alone but would require a demonstration that the discharge from the MS4 is causing or contributing to the lowered CSCI score. The Draft Staff Report Section 5.3.4 states (including emphasis):

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“Where conditions in the receiving waters subject to a discharge do not meet the Stream Biological Objective that result in itself does not produce a condition of permit noncompliance (emphasis added). Permits are issued to ensure that a discharge does not cause or contribute to an exceedance of water quality standards, including the Stream Biological Objective.”

The Draft Staff Report goes on to recognize that there may be other factors that cause or contribute to the objective not being met:

“It is possible that factors external of the permitted discharge result in the Stream Biological Objective not being met in a receiving water, such as illicit discharges, illegal dredge or fill activities, noncompliance by other permitted dischargers, or natural factors.”

The SED Section 1.4 further clarifies the intended use of the objectives (emphasis added):

“Biological Objectives are expected to provide clarity in the implementation of compliance measures to meet existing Beneficial Uses by providing the information to focus on specific pollutants causing impacts to beneficial uses, as well as incorporating considerations of site-specific habitat conditions.

Section 5.3 of the Draft Staff Report confirms that the intent (i.e., to control the pollutant(s) in the discharge identified to be causing or contributing) is consistent with the Clean Water Act Section 402 which “establishes the NPDES Program to regulate the ‘‘discharge of a pollutant,’’ other than dredged or fill materials, from a ‘‘point source’’ into ‘‘waters of the U.S.” (CWA §§ 1342(a) & 1362(12)).” The proposed BPA should be explicit and consistent with these stated intentions to regulate the discharges found to be causing or contributing to CSCI scores that are not meeting the water quality objective.

Recommendation: To address this concern, language should be incorporated into the BPA for Chapter 4, Section VI.A in the opening paragraph to state that “MS4s are only responsible for addressing pollutants causing or contributing to lowered CSCI scores to the Maximum Extent Practicable.”

5.2 Receiving Water Limitations

The intent of the proposed policy is to regulate pollutants that may be impacting beneficial uses, as illustrated by a comparison of the CSCI to the Stream Biological Objectives; therefore, it is not necessary to incorporate the new objective as a receiving water limitation in the Phase I MS4 Permit. When low CSCI scores are identified, the required cause or contribute assessments will be performed, and in some cases, specific pollutants may be identified within the receiving waters and MS4 discharges that are impacting CSCI scores. Pollutants already have established water quality objectives in the Basin Plan, and since compliance is ultimately based on the pollutants that are causing or contributing, there is no need for another layer of potential receiving water limitations liability.

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Further, the process of informing and adapting programs takes time, and absent an implementation schedule (or use of the alternative compliance pathway under Provision B.3.c of the Phase I MS4 Permit), implementation of these objectives as receiving water limitations would cause immediate non-compliance with permit conditions and could cause long-term compliance issues for permittees. The biological objective can, and should, be used as a guidepost or feedback mechanism to assess the beneficial uses of the receiving waters and to inform the Water Quality Improvement Plan prioritization process and strategy selection, but it does not need to be incorporated as a receiving water limitation to do so. The SED indicates that Biological Objectives would be used to determine the prioritization of these compliance measures as well as to determine effectiveness under existing regulatory program requirements. It is unclear how this will be reconciled with receiving water limitation requirements that apply the “cause and contribute” standard in all locations at all times.

Recommendation: Do not set the proposed Biological Objectives as a receiving water limit in the Phase I MS4 Permit. Additionally, the compliance discussion in the proposed Chapter 4 BPA, Section VI.A, should clarify what is meant by the “alternative compliance pathway option” as this terminology is also often used in the sense of land development. A reference should be added to refer to Provision B.3.c of the current Phase I MS4 Permit for San Diego.

5.3 Channel Modifications

Draft Staff Report section 3.3.4 notes that altered channel morphology is an example stressor that can reduce biotic richness in the stream. This can be in the form of “hydraulically efficient (engineered) drainage systems.” Section 5.1 goes on to state (emphasis added):

“For those discharges to receiving waters where other sources, such as in-stream channel hardening, already cause and/or contribute to an exceedance, the permitted discharge is largely not required to remedy existing instream physical habitat condition in order to discharge (see discussion in Section 5.5) unless a condition of proposed mitigation associated with a site-specific project (e.g. Section 5.6), or as a matter of enforcement (e.g. illegal fill). Instead, the discharger would be, consistent with existing water quality objectives, required to ensure its discharge does not contribute to the continued degradation or increase the level of degradation, resulting in additional Beneficial Use loss (e.g. Section 5.2).”

Draft Staff Report Section 4.4.4 also states:

“Sites with no evidence of degraded conditions as confirmed by benthic algae, toxicity, and water chemistry results, but with evidence of physical habitat alteration that is impacting benthic macroinvertebrates, are good candidates for physical habitat restoration.”

This statement seems to encourage restoration in some circumstances. The concept is further explained in SED section 1.4.5 which indicates that instream restoration could be implemented as a voluntary element of a Water Quality Improvement Plan and other non-regulatory means, specifically as related to permittees:

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“Biological Objectives may also be used on a voluntary basis in Phase I municipal stormwater permitting should a permittee choose to proceed with the alternative compliance pathway for receiving water limitations under the permit. The alternative compliance pathway is not a mandatory requirement, but an option that allows permittee(s) to propose how they will set goals, implement programs, and measure compliance to meet receiving water limits. Alternative compliance may include voluntary in-stream habitat restoration should such actions be deemed suitable and feasible by the permittee(s) on a site-specific basis.”

The SED continues to re-iterate this approach:

“In some cases, for Biological Objectives to be achieved, in-stream habitat restoration will be conducted through the implementation of voluntary measures that are not regulatory in nature.

…these projects are not required nor undertaken for the purposes of compliance with Biological Objectives, though improvements in water quality are expected to occur, including for Biological Objectives, and individual projects may use biological assessments. As such, a discussion of these activities is included within the SED. These projects will be subject to their own environmental review, the statutory regulatory authority of the Water Boards, and it is not reasonably foreseeable to estimate the magnitude, scope, timing, and duration of such projects at this time.”

The County supports this approach but is concerned that violations related to receiving water limitations could lead to enforcement and required restoration actions if objectives are not met. The SED makes some statements that appear counter to the “voluntary” concept such as:

“reasonably foreseeable methods of compliance for Biological Objectives include additional monitoring and assessment requirements for dischargers, updated Best Management Practice and/or source controls consistent with existing permit requirements, and stream habitat restoration.”

This concern is reiterated by statements in Draft Staff Report Section 5.5:

“The existing San Diego Regional Municipal Storm Water permit (R9-2013-0001) includes requirements for redevelopment activities to mitigate for changes in hydrology associated with redevelopment projects. In addition, Section E.5.e of R9-2013-0001 requires Copermittees have a program to retrofit areas of existing development within its jurisdiction to address identified stressors, including pollutants and pollution, and to have a program for the rehabilitation of streams, channels, and habitats within areas of existing development in consideration of pollutants and pollution. These existing requirements are expected to gradually address pollution over time and allow for instream habitat restoration to occur at various time scales, due to difference in existing stream condition, independent of the traditional TMDL process.”

The Draft Staff Report and SED both acknowledge that low CSCI scores can be the result of stressors present in discharges and/or result from the effects of engineered or modified

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channels. NPDES Permits are intended to regulate discharges to receiving waters and should not include enforcement actions related to rehabilitation of engineered channels.

Recommendation: Understanding that low CSCI scores that result specifically from engineered or modified channels (i.e., pollution), as opposed to resulting from stressors present in discharges (i.e., pollutants), ultimately would not be addressed through an NPDES Permit, clarification should be added to Section 5.3 of the Draft Staff Report to ensure that use of restoration options would not be required through enforcement in the context of a Phase I MS4 Permit.

5.4 Probable Threat

MS4 discharges are presumed to be a “probable threat” to the beneficial uses supported by the proposed Stream Biological Objectives, so permit requirements are automatically included without further analysis. The proposed Chapter 4 BPA Section V.B.2 defines the term “probable threat” to mean: “the discharge is or has the potential to cause or contribute to a decrease in the CSCI score in the receiving water or downstream waters”. The Draft Staff Report also includes the concept of “probable threat” in Section 5.3.1, stating that “[F]or dischargers that are determined to present a probable threat, bioassessment will be required in surface waters subject to the discharge”. It goes on to state in Section 5.3.3 that “Phase 1 [MS4] discharges have already been determined by the San Diego Water Board to represent a probable threat to the Stream Biological Objective” and justifies this through findings in the current Phase I MS4 Permit (Order R9-2013-0001 as amended). This presumption deeming MS4s a “probable threat” should be removed from the Draft Staff Report for three primary reasons:

1. Based on our review of the Phase I MS4 Permit, there is no justification that all MS4 discharges meet the threshold of a “probable threat”. The statement is not supported in Order R9-2013-0001. Finding 14 in the Order does state that bioassessment data indicate that the majority of monitored receiving waters have Poor to Very Poor Index of Biotic Integrity (IBI) ratings and goes on to say that “[T]hese findings indicate that runoff discharges area causing or contributing to water quality impairments”. However, the finding stops short and is not supported by any discussion of causality related to the IBI scores – in the finding nor in the Fact Sheet (Attachment F of the Phase I MS4 Permit). As recognized above, and throughout the proposed policy, impacts to the benthic macroinvertebrate community are not limited to pollutant discharges. 2. The proposed policy is relying on the concept of “probable threat” to justify requiring implementation of monitoring and reporting related to the proposed Stream Biological Objective. However, as acknowledged in Section 5.3.3 of the Draft Staff Report, the current Phase I MS4 Permit already requires the permittees to use bioassessment monitoring and reporting to guide permit implementation actions. Current requirements include a cause or contribute assessment, which should be the determining factor as to whether discharges from MS4s are causing lower CSCI scores, not a general finding based on previous broad assessments of the data. Further, if the proposed Stream Biological Objective is maintained as a receiving water

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limit in the Phase I MS4 Permit, the Copermittees would again be required to assess if their discharge(s) are causing or contributing to an exceedance of the Stream Biological Objective receiving water limit and, based on that evaluation, adjust their BMPs in accordance with permit requirements. Because permittees are already required to use bioassessment in this way, and this will be further supported by the proposed Stream Biological Objective, there is no need to include an overbroad statement about “probable threat”. Cause or contribute assessments should stand on their own. 3. Permittees without an alternative compliance approach provided through Provision B.3.c may be exposed to litigation from third parties in many receiving waters throughout the region. The assumption that MS4s present a “probable threat” may make the assessment of impacts from MS4 discharges more arduous should the permittees desire to demonstrate that they are not the cause of the exceedance (or impairment). This shifts the responsibility to the permittees to demonstrate that they are not causing or contributing, rather than requiring the third party to positively demonstrate the linkage.

Moreover, Finding 7 in the Phase I MS4 Permit forbids that treatment control best management practices be constructed in a receiving water. Assuming that all MS4 discharges are a probable threat to degradation of the biological community of the stream, it is unclear how stream rehabilitation and restoration work conducted by permittees can be considered an allowable compliance strategy.

Recommendation: Remove statements regarding “probable threat” as related to the Phase I MS4 Permit. The concept may be useful in other contexts where monitoring and assessment requirements may need to be determined but should not be used in reference to Phase I permittees.

5.5 Basin Plan Implementation Language

The proposed Chapter 4 BPA is critical to successful implementation of the new policy. There are a few places where clarification is needed to provide clear direction for implementation. As drafted, it is unclear which requirements in Section V (Permitting) apply to permittees under the regional Phase I MS4 Permit. Section V.A.1 contains a clear statement that the “ROWD requirement[s] under this section are not applicable for Phase I MS4 or Agricultural dischargers, as special implementation requirements apply (see Section VI below)”. This type of statement, or the contrary (i.e., that a provision does in fact apply to the Phase I MS4 discharger) is lacking in Section V.B, creating ambiguity. It is unclear if the Basin Plan provisions in V.B are applicable to MS4 discharges. As written, it appears that implementation will rely on some combination of Sections V.B and VI.A. Recommendation: Clearly articulate all Phase I MS4 implementation requirements in Section VI.A to provide clarity.

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Section V.B.1 of the proposed Chapter 4 BPA addresses how discharge limits may be derived as related to the proposed Stream Biological Objectives. The language is clear that the proposed objectives shall be applied as a receiving water limit. The language goes on to say that the proposed objective “shall not be translated into or applied as an effluent limitation unless the following conditions are met:

A clear causal relationship has been established linking the discharge and nonattainment of the Stream Biological Objective,

The pollutants or physical factors causing or contributing to nonattainment of the Stream Biological Objective have been identified, and

Loading studies have been completed to estimate the reductions in pollutant loading for the discharge that will restore the beneficial use(s).”

These conditions focus primarily on the discharge, which could potentially have more than one pollutant. Although the second bullet does state that the pollutants causing or contributing have been identified, based on experience, this is often difficult to determine. Challenges associated with causal assessments can lead to elimination of certain pollutants as the cause but can leave others as potential. Where causal assessments are not definitive, effluent limitations should not be applied. Additionally, for the Phase I MS4 Permit, effluent limitations for identified pollutants would require an evaluation of CWC Section 13241 prior to being incorporated into the Phase I MS4 Permit. Recommendation: Add a footnote to the second bullet point to clarify that effluent limitations could only be developed for a pollutant identified through a causal assessment as contributing to the lowered CSCI scores and would not be developed for other pollutants just because they may be exceeding an objective (without identification of contribution through causal assessment) and that effluent limitations would only be included in MS4 permits after consideration of CWC Section 13241 factors. Table TBD of the proposed Chapter 4 BPA includes a requirement for the Phase I MS4 Permittees to notify the San Diego Water Board 12 months prior to submittal of the ROWD if they intend to use the “alternative compliance pathway option” to comply with the receiving water limitations. Phase I MS4 Permittees may not be able to elect to use the alternative compliance pathway option prior to development of the ROWD and may determine at a future date based on new data to elect the pathway to comply with biological objective receiving water limitations, if included in the Phase I MS4 Permit. The Phase I MS4 Permittees should have the flexibility to determine at any time that the alternative compliance pathway will be used as needed for compliance. Furthermore, considerations in the timing for the election of B.3.c as a pathway should be addressed in the Phase I MS4 Permit and not in a BPA. Recommendation: Remove the requirement in Table TBD to notify the San Diego Water Board about the intent to use the alternative compliance pathway option.

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The SED and Draft Staff Report acknowledge that multiple decades may be necessary for all waterbodies to attain the biological objectives, but no expectations for the time frame for attaining the objectives is included in the Chapter 4 BPA. Without any reference to an implementation timeframe, the BPA implies that the objectives will be attained when the BPA becomes effective. The Chapter 4 BPA should include a discussion acknowledging that a significant amount of time is anticipated to be needed to bring all waterbodies into attainment with the objectives. Recommendation: Include a new section entitled Anticipated Time Schedule for Attaining the Stream Biological Objective. In the section, include language from the SED and Draft Staff Report regarding the expected time frame for the waterbodies to attain the objectives. Additionally, the BPA should allow for compliance schedules to be included in NPDES permits to provide time for dischargers to meet new permit requirements associated with the biological objectives.

6. Selected Reference Threshold is not Appropriate for the San Diego Region

The County has a number of technical concerns with the selection of a numeric threshold for the objective and its expression in the Basin Plan.

6.1 Selection of 10th Percentile of Reference Conditions is Not Linked to Beneficial Use Protection

The cited report used as the basis for selecting the 10th percentile of reference conditions as the objective, Mazor et al 2016, is a document describing the development of the CSCI index. In that document, different bins of waterbody condition were created to evaluate the accuracy of the index. “We created 4 condition classes based on the distribution of scores at reference

calibration sites, with a recommended interpretation for each condition class: likely to be intact (>30th percentile of reference calibration site CSCI scores), possibly altered (10th–30th percentiles), likely to be altered (1st–10th percentile), and very likely to be altered (<1st percentile).”17

No information is provided in the manuscript linking these thresholds to beneficial use protection nor is there any justification provided for the selection of the bins. As noted by the Science Panel, use of a statistical distribution alone is not recommended for developing objectives. Biological endpoints, supported by statistical analyses, are needed to provide the linkage to beneficial uses. The reference cited only provides one opinion of a threshold that represents a likely deviation from reference conditions with no consideration of natural temporal variability. As noted in the Draft Staff Report and evidenced by the numerous other thresholds chosen by other states for objectives, the 10th percentile is not the only percentile that could be chosen for determining the objective. The justification provided in the Draft Staff Report is insufficient to warrant a numeric objective. Additionally, the proposed objectives do not have any method to account for year-to-year

17 Mazor et. al. 2016 page 259.

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variations caused by short-term natural conditions, such as drought, or long-term conditions such as climate change. During drought and other natural conditions, the reference dataset appears to have depressed scores that are not accounted for within the objectives. Additionally, the averaging period and allowable frequency of exceedance for the objectives have not been established. These components are outlined in USEPA’s Water Quality Standards guidance as components of water quality criteria that should be established when setting objectives.

6.2 Selected Value of 0.79 CSCI Threshold is not Appropriate for the San Diego Region

The benthic macroinvertebrate community is being used as the single line of evidence to assess biological integrity and the protection of aquatic life beneficial uses, and the CSCI is the metric being used to measure the benthic macroinvertebrate community health. To determine the CSCI score for any individual stream site being sampled, a “modeled reference site” is developed using the distribution of a sub-set of unaltered analogous streams from the statewide reference pool. This sub-set of reference streams are those selected from the statewide reference pool that are most analogous (similar) to the individual stream being sampled in terms of latitude, longitude, elevation, watershed area, long-term temperature and precipitation, and underlying geology.

While the CSCI score for an individual site sample is derived from analogous reference streams, the CSCI numeric objective threshold of 0.79 is derived from the 10th percentile of the entire statewide reference pool data set distribution. This statewide distribution contains many non-analogous reference sites, as the statewide reference pool encompasses sites from all regions of California, including extreme northern California and the Sierra Nevada Mountains which are much different than reference streams in xeric southern California. Including sites from these other non-analogous regions in the pool used to derive the numeric criteria skews the 10th percentile of the distribution upward, resulting in an overly conservative CSCI threshold of 0.79 for the San Diego Region xeric streams. This topic was addressed by Dr. Mazor of SCCWRP during the Public Workshop on May 15, 2019. Dr. Mazor indicated that if only the state bioassessment sites were used for the San Diego Region, then in fact a more conservative value than even 0.79 would result. This appears to be because so many of the reference sites in the San Diego region are in the mountains at high elevations. However, Dr. Mazor did indicate that looking at a wider area of southern California than just San Diego would result in a less conservative value. This alternate approach further discussed below is requested to be considered in lieu of the proposed 0.79 CSCI threshold.

A more appropriate regional CSCI numeric objective would be derived from streams physically, hydrologically, and geographically most similar to San Diego Region streams. Figure 3 of the Mazor et al (2016) paper describing the development of the CSCI, distinguishes the South Coast xeric (Group 8) and mountains (Group 10) as distinct biological clusters. Results of the CSCI analyses for a typical San Diego region stream shows two clusters as overwhelmingly the most “analogous” within the statewide reference pool. The 10th percentiles for these two clusters are 0.66 (Group 8) and 0.80 (Group 10). By combining these two more appropriate reference groups for the San Diego Region, the 10th percentile CSCI numeric objective threshold would be closer to 0.69.

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The technical justification for using a single statewide threshold (as provided in the Draft Staff Report Appendix 1, S1) is the lower error rate of the predictive model (the current CSCI model) versus the null model (non-predictive model), with the error rate being the percent of sites considered reference that fall below the 0.79 threshold. While the predictive CSCI model did bring down the error rate, the South Coast sites used in this analysis are a composite of South Coast mountain and xeric locations. In Figure 4 of the Mazor et al (2016) paper, the South Coast mountain and xeric regions are separated for analysis purposes. These two regions have among the largest variability in reference O/E and CSCI scores, and validation data suggests that the South Coast mountain reference sites are biased upwards, while the South Coast xeric (coastal) reference sites are biased downward. If the same analysis performed in Appendix S1 were performed separately on South Coast xeric and mountain sites, the results might look much different.

Additionally, many states, some much less geographically and climatically diverse than California, have recognized the need for regional thresholds within their state to accommodate the various differences in ecoregion, geography, or habitat type as detailed earlier in this letter A guiding principle of the State Water Board’s Biostimulatory-Biointegrity Project should be taken into consideration regarding the previous discussion: “There should be statewide consistency with eco–regional flexibility. Statewide consistency is important for equity among stakeholders; however, the State has many different ecosystems, each of which has varying biological characteristics. Therefore, a defensible statewide program must accommodate the unique qualities of each ecoregion.” Providing statewide consistency and equity among stakeholders does not mean that there has to be one blanket threshold applicable to all regions, but rather that all regions are treated equally in terms of the appropriateness and fairness of the threshold. Currently, using the 0.79 CSCI threshold statewide does not provide equity among stakeholders, as sites in the South Coast, particularly the xeric South Coast are at a disadvantage. Reference sites most analogous to each sampled site is information already available as an output of the CSCI scoring tool, and could be used as the basis for determining the 10th percentile of analogous reference sites threshold.

Additionally, inclusion of a specific value of 0.79 in the BPA is not consistent with the objective that is stated as the 10th percentile of analogous reference sites. As additional data and refinement of reference sites is developed over time, especially in light of climate change impacts, the 10th percentile value may change. This is supported by discussion in the Draft Staff Report that allows for adjusting the numeric value of the objective over time if reference conditions change.

“The pool of reference sites can be augmented by the State or other interested entities (e.g. Stormwater Monitoring Coalition, NGOs), and can include repeated sampling over time at selected sites, which will both increase precision and allow for incorporation of predicted reference condition change over time if influenced by external factors, such as climate change.”18

Including 0.79 in the Basin Plan would require a BPA to change the numeric value of the 10th percentile and prevent easy incorporation of new science and reference changes.

Recommendation:

18 Staff Report, page37.

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If the San Diego Water Board elects to adopt a single threshold then change the proposed numeric threshold from 0.79 to 0.69, to better represent the dry portions of southern California. Include the threshold in Chapter 4, rather than Chapter 3 to allow for the threshold to be modified without a BPA if needed to incorporate new science and reference conditions. Furthermore, the San Diego Water Boards should consider a range of scores as acceptable to consider natural variability and climate change.

7. Technical Challenges Exist With Implementing and Attaining the Objectives

Much of the implementation approach relies on the ability to determine if dischargers are causing or contributing to lowered CSCI scores and identify the causes of the lowered scores. However, there are technical challenges with the available tools, and it may not be possible to make these findings. The objectives do not provide any off-ramps or mechanisms to address situations where the causes cannot be clearly identified, or restoration does not achieve expected results.

Under routine NPDES permit compliance, where stream benthic communities are considered as not meeting biological objectives, the San Diego Water Board in the Draft Staff Report highly encourages the use of rapid causal assessment methods as part of their implementation. Furthermore, rapid causal assessments may be required by dischargers for source identification monitoring and assessment if receiving water monitoring continuously indicates a discharge may be causing or contributing to an exceedance of numeric biological objectives when compared to upstream monitoring results. The implementation approach relies on the ability to determine if dischargers are causing or contributing to lowered CSCI scores and then identifying the causes of the lowered scores. However, the policy seems to oversimplify the ability to determine the causes of lowered CSCI scores and implement strategies to address those causes. The 2012 pilot program under the State’s original Biological Objective Program demonstrated that EPA’s Causal Assessment procedures, while scientific and thorough, were much better at ruling out causes of impairment than determining the cause of impairment. More recent efforts to improve and streamline this procedure have been undertaken by SCCWRP and the City of San Diego, however these methods are still under development and their effectiveness at determining the cause of benthic macroinvertebrate community degradation is still in question. Thus, it may be premature to have a regulation that includes numeric biological objectives that depend upon these tools for evaluating the causes of the biological impairments, until they can be further validated.

Furthermore, even if a likely cause(s) is identified and the stream is restored, it does not mean it necessarily attains 0.79 CSCI score. In fact, research has shown that restoration of streams in highly urbanized settings has had limited success. While many factors come into play when restoring an urbanized stream including sufficient reduction of water quality pollutants and reintroduction of appropriate habitat complexity, many streams that have reached these quality standards remain with minimal to no uplift in the benthic macroinvertebrate community condition. Recent research has shown that one of the factors often overlooked in restoration is the proximity of quality benthic macroinvertebrate source populations. A recent meta-analysis of 18 stream restorations in Maryland found that biological uplift at a location buried in a landscape of degraded stream habitats is unlikely to occur as there is no opportunity for

Mr. Loflen May 31, 2019 Page 29 of 37

species adapted to natural environments to reach this location19, and that if it does occur, this uplift would occur in a decadal scale rather than the typical 5-year term designated under most permit follow-up monitoring programs. Many other studies have found similar results in terms of both the probability of recovery and time-scale predictions.

These research findings reveal that the restoration goals outlined can hold a permitted agency to a standard that is likely not attainable within a reasonable timeframe, if at all. An understanding of the constraints and “biological ceilings” not only placed on benthic macroinvertebrate communities located in highly urbanized and modified streams, but also the limited restoration potential should be outlined in the policy, and appropriate restoration goals or alternatives should be considered for these urbanized systems.

Recommendation: The limited restoration potential of highly urbanized streams should be outlined in the policy, and appropriate restoration goals or alternatives should be considered for these urbanized systems. Remove requirements for restoration projects to only be considered successful if they attain the water quality objective.

7.1 Integrated Reporting and TMDL Clarifications

Inconsistencies exist between Chapter 4 of the BPA and discussion in the Draft Staff Report and SED about how the biological objectives will be used for integrated reporting and TMDL development. The Basin Plan Language should be aligned with the Draft Staff Report and SED. In particular, the Chapter 4 language should:

1. Reflect the discussion in the SED on page 124 that biological objectives will only be used as a TMDL goal (not a target).

2. Clarify that Category 4c listings will not be included as a NPDES permit requirement because they are not associated with a pollutant.

Recommendations: Modify Basin Plan Chapter 4.IV.A.1 as follows:

If data shows the impairment is not associated with the discharge of a pollutant (i.e. physical habitat and/or hydrologic impairment only), the San Diego Water Board will consider non-TMDL and non-NPDES permit approaches to address the impairment.

The San Diego Water Board will use the Stream Biological Objective to establish a minimum restoration goal or target for the TMDL or TMDL Alternatives …

7.2 Incorporation of Biological Objectives in 401 Permits

The County implements infrastructure maintenance projects in currently developed areas that sometimes impact small areas of urbanized waters which are typically ephemeral or intermittent.

19 Southerland, M., C. Swan, and A. Fortman. Meta-Analysis of Biological Monitoring Data to Determine the

Limits on Biological Uplift from Stream Restoration Imposed by the Proximity of Source Populations. Personal

communication. Unpublished paper.

Mr. Loflen May 31, 2019 Page 30 of 37

To ensure no net loss of waters, the County restores waters onsite or offsite. The small size, disturbed nature, and dry conditions make benthic macroinvertebrate analysis infeasible for these sites in most cases. However, benthic macroinvertebrate analysis is a standard condition in 401 Permits. Making a change to this standard condition becomes difficult when the San Diego Water Board 401 staff does not have the expertise to determine when this protocol is or is not feasible. Therefore, the County recommends that the ideas presented in Table TBD of Chapter 4 (Implementation) be incorporated into the standard 401 template for projects in Southern California (Region 9). Specifically, the 401 template should provide guidelines when Stream Biological Objectives do not apply and when CSCI as a performance target for compensatory mitigation is not appropriate. Recommendation: The 401 template should provide guidelines when Stream Biological Objectives do not apply and when CSCI as a performance target for compensatory mitigation is not appropriate.

8. Substitute Environmental Document is Incomplete

The State Water Board’s CEQA implementation regulations describe the environmental documents required for BPA actions (CCR, tit. 23, § 3720 et seq. “Implementation of the Environmental Quality Act of 1970.”). Pursuant to California Code of Regulations title 23 section 3777, any water quality control plan, State policy for water quality control, and any other components of California's water quality management plan as defined in Code of Federal Regulations, title 40 sections 130.2(k) and 130.6, proposed for board approval or adoption must include or be accompanied by an SED and supported by substantial evidence in the administrative record.

As written, the SED supports inclusion of Biological Objectives as a helpful indicator of water quality in perennial and seasonal streams, but is lacking in details needed to fully understand the consequences of implementation, and thus, it is not adequate, complete or a good faith effort of full disclosure (CCR, tit. 14, § 15151) to support the adoption of the Biological Objectives. The following paragraphs provide additional details to support this conclusion. Table 1 of the SED provides a list for reasonably foreseeable compliance measures to meet the intent of the Biological Objectives. These compliance measures include additional sampling, structural and nonstructural BMPs, focused source control, enforcement via cleanups of unpermitted discharges to streams and stream habitat restoration. The analysis in the SED should clearly designate the actions in Table 1 as Environmental Change Subject to Review impacting each environmental topic (e.g, p 30, Aesthetics, Biological resources, hydrology/water quality, noise, recreation). For example, habitat restoration has the potential to impact many resources such as visual aesthetics, recreational park usage, wetlands, cultural and tribal, and emission however, the SED states no impact would occur. Where impacts and mitigation measure are incorporated or discussed, the determination is still “no impact” which appears inconsistent. Many environmental factors have the potential

Mr. Loflen May 31, 2019 Page 31 of 37

of being impacted however, the SED only indicates that biological factors have the potential to be impacted.

The impacts of the Adoption of Biological Objectives have been stated as they “will not cause any change in the type of compliance methods that have been implemented to address discharges of pollutants or restore stream habitat (page 27).” Although the types of compliance methods may not change, the adoption of biological standards could require compliance methods that were not originally required. If a receiving water was not considered impaired under previous standards (chemical and physical), but does under the new biological objectives, the permittee may be required to employ compliance methods not originally required. These additional measures could have adverse impacts to the surrounding habitats if they result in changes to project footprint or designs or implementation of measures currently not required such as additional BMPs. Additionally, although types of compliance are not changing, the intensity of implementation is changing and this has not been thoroughly considered for each of the environmental topics. The SED states that the San Diego Water Board does not specify actual means of compliance (page 28), but their new objectives could require the permittee to employ these means of compliance. The San Diego Water Board defers any analysis of these means of compliance and their impacts to the permitting agency. The San Diego Water Board acknowledges that “this evaluation makes no attempt to quantify the impacts associated with implementation or maintenance of a particular compliance method.” As these Biological Objectives may increase permit conditions and requirements, the Biological Objectives can indirectly affect the magnitude of implementation and maintenance actions. Since these permits are often issued after CEQA is completed, the compliance activities would never be analyzed under CEQA. This document falls short in not analyzing these impacts. The SED notes that there is a “Less than significant with mitigation incorporated” impact to biological resources. The SED states that all activities associated with or as a result of the Biological Objectives is already handled by existing regulatory agencies. The SED indicates that these measures would be required regardless of the Biological Objectives. However, as the Biological Objectives are new standards, they could increase the amount of mitigation required and change the type of mitigation employed. As these Biological Objectives are expected to be more stringent than existing standards, it only seems reasonable that more mitigation would be required.

Specific areas where the SED analysis needs improvement are listed in Table 2.

Mr. Loflen May 31, 2019 Page 32 of 37 Table 2. Summary of Incomplete Analyses Identified in SED

Resource Area San Diego Water

Board

Determination

Page #

of SED

Issue

Impact Methodology -

Site Specificity

Does not address

site specific

impacts

27 Defers impact analysis to other

agencies

Impact Methodology -

Change in Type of

Compliance

No change in

Type of

Compliance

Measures

27 Does not address changes in

magnitudes of compliance measures

not additive effects of multiple

measures

Impact to Biological

Resources

Less than

significant with

mitigation

measures

43 Does not discuss mitigation measures

impacts, defers to regulatory agencies

Impact of Biological

Monitoring

No impact 50 Impacts to habitat from monitoring not

analyzed, deferred to regulatory

agencies

Cultural Resources No Impact 52 Ground disturbance and grading to

comply with increased mitigation

measures could impact cultural

resources

Impact to

Utilities/Service

Systems

Less than

significant with

mitigation

measures

92 Defers impacts associated with newly

required facility upgrades to other

agency permits

Final Conclusion Could Not have a

significant effect;

No mitigation

required

95 Inconsistent with findings in Biology,

Utilities, GHG, Hydrology,

Transportation - all had mitigation

measures

Recommendation:

Increase the robustness of the analysis of possible environmental impacts and

mitigation measures from the compliance activities anticipated to be required to

comply with the Biological Objectives in order to meet adequate, complete or a good

faith effort of full disclosure (CCR, tit. 14, § 15151) that is required of the analyses

presented in a SED.

Mr. Loflen May 31, 2019 Page 33 of 37

9. Proposed Objectives Do Not Meet CWC Section 13241 Requirements

The proposed BPA would establish a water quality objective (i.e. “formal minimum standard”) for surface waters in the region which requires attainment of a CSCI score of 0.79. The BPA, Draft Staff Report, and SED are clear that, where discharges are determined to cause or contribute to degradation (i.e. a CSCI score of less than 0.79), permit and TMDL requirements will be established which require attainment of this CSCI index value in those waters. These proposed actions raise serious issues with regard to the San Diego Water Board’s fulfillment of requirements stipulated in the CWC that are associated with the establishment of water quality objectives. Section 13241 of the CWC requires that:

“Each Regional Water Board shall establish water quality objectives in water quality control plans as in its judgment will ensure the reasonable protection of beneficial uses and the prevention of nuisance; however, it is recognized that it may be possible for the quality of water to be changed to some degree without unreasonably affecting beneficial uses. Factors to be considered by a Regional Board shall include, but not necessarily be limited to, all of the following: (a) Past, present, and probable future beneficial uses of water.

(b) Environmental characteristics of the hydrologic unit under

consideration, including the quality of water available thereto.

(c) Water quality condition that could reasonably be achieved from the

coordinated control of all factors which affect water quality in the area.

(d) Economic considerations.

(e) The need for housing within the region.

(f) The need to develop and use recycled water.”

Section 13242 of the CWC requires that: “The program of implementation for achieving water quality objectives shall include, but not be limited to: (a) A description of the nature of actions which are necessary to achieve

the objectives, including recommendations for appropriate action by any entity,

public or private.

(b) A time schedule for the actions to be taken.

(c) A description of surveillance to be undertaken to determine compliance

with objectives.”

The SED includes text which purports to address CWC Section 12341 requirements; it does not address CWC Section 13242 requirements. The subject text describes the regulatory mechanisms (permits, TMDLs, non-TMDLs, enforcement actions) that would be used to compel dischargers to achieve the proposed water quality objective. The text also makes general reference to actions that would be employed (e.g. monitoring, pollutant and flow controls, in-stream restoration actions). The SED implies, but does not demonstrate, that all waters in the region will eventually meet the proposed objective. This information is insufficient in fulfilling the requirement of Section 13241.

Mr. Loflen May 31, 2019 Page 34 of 37

With regard to the requirement of Section 13241 (a), the SED fails to address the fact that some waters of the region do not currently achieve, and may not “probably” achieve, the beneficial use defined by attainment of the CSCI index score of 0.79. This failure to clearly acknowledge and quantify the status of beneficial uses is a fundamental flaw which hampers the overall Section 13241 and Section 13242 analysis offered in the SED. Such a determination would require consideration of actual data for waters in the region and quantification (e.g. an estimate) of the percentage of waters that do and do not currently meet the objective. With regard to the requirement of Section 13241 (c), the SED falls far short of a credible assessment of the achievability of the proposed objective in all waters in the region. As a first step, the assessment should include a determination whether the objective is currently achieved in all waters (i.e., fulfillment of Section 13241 (a) requirements, as described above). As a next step, the assessment should include information regarding the ability for waters that do not currently meet the objective to achieve the objective as a result of remediation actions. This information should be based on some form of tangible analysis, e.g. case examples where such results have been observed to occur and information to indicate that remediation measures will be effective. The assessment must also include an analysis to demonstrate whether such measures are reasonable (i.e. feasible, proven, cost-effective, affordable). Finally, the assessment should identify waters that are not expected to ever meet the objective. This finding should inform the program of implementation for such waters, as required under Section 13242. With regard to the requirement of Section 13241 (e), the SED includes arguments that the adoption of the BPA will not increase costs due to savings that will occur due to a reduction in existing permit and TMDL requirements. These arguments are non-specific and include questionable assumptions regarding (a) the ability to identify causative factors for water bodies which do not attain the desired CSCI value of 0.79 and (b) changes in existing requirements (e.g. chemical specific NPDES permit or TMDL requirements) as a result of implementation of the proposed biointegrity objective. With respect to (a), there is little evidence that causal assessments will yield specific solutions that lead to attainment of the proposed objectives. With respect to (b), such changes require significant regulatory actions which may or may not be approved and implemented. Therefore, the assumed economic benefits of the proposed objectives are unlikely to occur, and the economic analysis provided in the SED is insufficient in its detail and conclusions. Recommendation: Modifying the proposed objectives to a phased approach based on the County-proposed Antidegradation Alternative would allow for existing information to be utilized to address the concerns outlined above. Additional information could then be developed as part of the second phase of the project to support evaluation of the need for and identification of appropriate objectives for waterbodies that are covered by antidegradation objectives.

Mr. Loflen May 31, 2019 Page 35 of 37

10. Additional Clarifications and Questions

In addition to the comments above, the County has a number of questions and clarifications on the documents that should be addressed before the objectives are considered for adoption.

10.1 Unclear Scope of Sampling and Spatial Representativeness of Scores

The Draft Staff Report is silent as to how many samples and over what timeframe benthic community condition needs to be demonstrated for a reach to be considered impaired. The State currently has specific guidance for how multiple site/event data should be compiled to make regulatory assessments. The State’s May 2010 Workplan for Developing Biological Objectives for Perennial Wadeable Streams in the State of California states,

“Topics such as how many sites are needed per waterbody, how many sample events over what period of time, the precision or error inherent in the stressor response model, and how large the magnitude of impairment, should all be factors used to decide if a site is defined as biologically impaired.”

Additionally, the Draft Staff Report does not specifically state whether benthic macroinvertebrate data collected outside of the recommended index periods would be considered in an assessment of impairment.

Similarly, more guidance is required to define what spatial extent is represented along a stream reach by a CSCI score. The California Stormwater Quality Association (CASQA) contracted SCCWRP to evaluate the spatial variability of bioassessment monitoring to determine the distances that CSCI values could be extrapolated beyond single-site observations (Mazor et al., 2017)20. The spatial stream network (SSN) models utilized did not support a general extrapolation distance that works in all settings given the large variability observed among and within watersheds. Rather, the study found that SSN models offer a way to support management decisions by creating maps of site-specific and spatially extrapolated CSCI scores along a drainage network. The Biological Objectives for the San Diego Region would benefit from applying this developing science.

10.2 Unclear how the Example Waterbody Prioritization is Aligned with the Compliance Requirements

The County appreciates the discussion in the Chapter 4 Basin Plan language and the Draft Staff Report about potential prioritization options for different waterbodies that could be used in the Water Quality Improvement Plan. However, the County is unclear on how this can be implemented if receiving water limitations are included in the Phase I MS4 Permit. Because the receiving water limitations require the same objective to be obtained in all waterbodies, how can different priorities be utilized in a Water Quality Improvement Plan and obtain compliance with the permit requirements? It seems that the alternative compliance pathway (Provision B.3.c of Phase I MS4 Permit) would be the only mechanism for obtaining compliance with the receiving water limitations and that provision requires a quantitative

20 Mazor, R., P.R. Ode, A.C. Rehn, and E.D. Stein. 2017. Spatial stream network (SSN) models to estimate the spatial representativeness of bioassessment samples. March.

Mr. Loflen May 31, 2019 Page 36 of 37

demonstration that the objectives will be attained. If non-pollutant discharges are contributing to the lowered CSCI scores, how can the alternative compliance pathway coverage be attained? The objectives set the expectation that all waterbodies will attain reference conditions at some point in the future and the implementation provisions in Chapter 4 do not provide any clarification that different approaches or expectations will be set based on existing waterbody constraints. The County is concerned that the proposed objectives would make evaluating, prioritizing and explaining required actions to the public and decision makers challenging when potentially unattainable numeric objectives are applied to urbanized waterbodies.

10.3 Discussion of Natural Conditions is Inconsistent between Chapter 3 and Chapter 4 Basin Plan Language

The proposed Chapter 3 Basin Plan language states: Alternative analytical methods approved by the San Diego Water Board are allowed for determining compliance if the cause of a low CSCI score is natural in origin. Alternative methods include other indices of biological integrity or physical habitat and sediment or water chemistry.

The proposed Chapter 4 Basin Plan language states:

Compliance Determination: San Diego Water Board must make the determination that the CSCI is inappropriate due to natural conditions. If this finding is made, the Compliance Determination section in Chapter 4 does not apply. The differences between the two chapters should be resolved. If the cause of the lowered CSCI score is natural, the objective should be considered attained and alternative indicators should not be needed. This is the approach proposed in the Statewide Biological Objectives Framework prepared by the State Water Board (see example flow chart in the attachment).

10.4 The Draft Staff Report and Chapter 3 Basin Plan Language are Unclear as to whether the Objective is Narrative or Numeric or the Time Period for Applicability of the Objectives

The Chapter 3 Basin Plan language appears to be a narrative objective with a numeric compliance threshold, but the Draft Staff Report states that 0.79 is a numeric objective. Please ensure the Draft Staff Report is consistent with the Basin Plan Language. The Proposed Biological Objectives were developed based on monitoring data collected in accordance with required sampling protocols. As noted in the Draft Staff Report:

“For the Stream Biological Objective, samples should be collected when streams are at or near base flow (i.e., not influenced by storm runoff), as sudden flow increases can displace benthic organisms from the stream bottom and dramatically alter local community composition (Ode et al. 2016b). State of California methods require sampling be carried out at least two, and preferably, three weeks after any storm event that has generated enough

mailto:Joann.Weber@sdcounty.ca.gov

Attachment

Recommended Revisions to the Proposed Amendment to the Water Quality Control Plan for the San Diego Basin to Establish Biological

Water Quality Objectives for Perennial and Seasonal Streams

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Chapter 3 – Stream Biological Objective Language

Biological Objective for Perennial and Seasonal Streams

Perennial streams shall support biological conditions consistent with unaltered reference streams. Compliance with this narrative objective is determined using the California Stream Condition Index (CSCI). CSCI scores less than the 10th percentile of the reference calibration sites do not meet the biological objective. However, where the cause of a low CSCI score is natural in origin, the waterbody is considered to be attaining the biological objective.

WATER QUALITY OBJECTIVES 3 - TBD

Formatted: Indent: Left: 0.08", Right: 0.1", SpaceBefore: 4.65 pt

Deleted: and seasonal

Deleted: 1

Deleted: compliance with

Deleted: may be determined using an alternate analytical method approved by the San Diego Water Board

Deleted: Alternative analytical methods include, but are not limited to: “Algal Index of Biotic Integrity for Southern California Streams” scores, “California Rapid Assessment Method” (CRAM) scores, and sediment or water chemistry.¶

Deleted: ¶Table TBD. CSCI Score Threshold for Perennial and Seasonal Streams¶¶Threshold CSCI Score 10th Percentile or Greater ≥ 0.79¶¶

Deleted: FN 1 For the purpose of this objective, “seasonal streams” means freshwater streams that are expected to be inundated with flowing water for at least four weeks between the months of February and October, except during periods of atypical or extreme drought. Seasonal streams have sufficient flows to conduct bioassessment sampling for stream aquatic benthic macroinvertebrates in most years. Seasonal streams do not include those streams that only exhibit ephemeral flow, which is flow that occurs only during or immediately following (e.g. 24-48 hours) rainfall events.¶

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

1

Basin Plan Chapter 4 Implementation:

New Section:

I. Introduction Biology based water quality objectives, or biological objectives, are a critical component of the

San Diego Water Board’s regional water quality assessment and management strategy.

Previously, San Diego Water Board programs operated under the paradigm that assessing the

chemistry of discharges and receiving waters would be sufficient to restore or protect water

quality. While a chemistry-based approach has been successful in certain instances for certain

beneficial uses, it has a constrained effect for the protection and restoration of aquatic life

beneficial uses1. Adoption of biological objectives takes a more holistic approach to water quality

because biological objectives provide a metric to assess the relationship between chemical,

physical, and biological conditions. Implementation actions to comply with applicable biological

objectives must consider the relationship between existing chemical and physical conditions as

well as the impacts that potential changes to these conditions may have on aquatic life beneficial

uses. Regulatory and permitting actions taken to comply with a biological objective will improve

prioritization of existing board programs and resources by focusing on the most important

chemical and/or physical conditions impacting beneficial uses.

The San Diego Water Board has adopted a biological objective for perennialand seasonal

streams (Stream Biological Objective). The Stream Biological Objective establishes a numeric

target for perennial and seasonal streams to achieve reference conditionsprotect beneficial uses, 2 as measured by the California Stream Index (CSCI).3 The CSCI uses benthic macroinvertebrate

data to quantify whether, and to what degree, the ecology of a stream is altered from a reference

condition. CSCI scores range for 0 (most stressed) to 1 or greater (similar to reference condition).

Typically, increases in human activity such as roads, housing, and agriculture are associated with

lower CSCI scores. The Stream Biological Objective is applied in addition to existing chemical,

physical, or toxicological water quality objectives. The Stream Biological Objective provides a

direct measure of attainment of designated aquatic life beneficial uses in perennial and seasonal

streams.

The San Diego Water Board has developed the following implementation program framework to

integrate the Stream Biological Objective into the San Diego Water Board’s regulatory programs.

The framework shown in Figure TBD will be utilized to implement the Stream Biological Objective.

Where the Stream Biological Objective does not apply, the San Diego Water Board may still use

biological monitoring and reporting on a case-by-case basis to assess attainment of designated

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

2

aquatic life beneficial uses where appropriate (e.g., identifying stressor and sources of

impairments, setting targets and goals for restoration of aquatic life uses, calculating and

assessing harm/potential to harm).

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

3

Figure TBD. Example Framework Flowchart from Biological Objectives for California’s Perennial Streams: Results from Pilot Study, Assessment

Framework & Regulatory Outcomes Presentation September 2011 (This is just a placeholder example of the type of framework flowchart that

should be included to define how the objectives will be implemented)

13

Assessment and Regulatory Outcomes Framework

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

4

II. Defining the Numeric Compliance Threshold The 10th percentile of the reference calibration sites shall be determined using analogous

reference sites applicable to the San Diego Region. The 10th percentile of reference calibration

sites is being established as an initial CSCI score of 0.69. The CSCI score for the 10th percentile

of reference calibration sites will be reviewed at a minimum every five years and consider any

new data from sites that meet reference site criteria applicable to analogous sites for the San

Diego Region. Modifications to the CSCI score for the 10th percentile of reference calibration

sites can be approved by the Executive Officer of the San Diego Water Quality Control Board

after consideration of comments obtained through a public comment period.

II.III. Time Schedule for Implementation Regulatory Actions to Implement of the Stream Biological Objective

This section outlines the time schedule for the implementationconducting regulatory actions to

implement of the Stream Biological Objective. In order for the Stream Biological Objective to be

achieved, the following types of implementation actions are required:

1. Monitoring and assessment specific for the Stream Biological Objective (General

Monitoring and Assessment).

2. Actions to protect and restore conditions when the Stream Biological Objectives are

or are not met (Planning).

3. Actions to ensure regulated discharges meet the Stream Biological Objective

(Permitting).

The time schedules for these implementation types, and their individual San Diego Water Board

program components, are outlined in Table TBD5. “Effective Date” means the date the Stream Biological Objective is approved by USEPA pursuant to Clean Water Act (CWA) section 303(c)(3).

A. Anticipated Time Schedule for Attaining the Stream Biological Objective Many streams have had historical physical habitat alteration for the purposes of the protection of

human health or property due to flooding associated with past land use development practices.

These practices often focused on modifying stream hydrographs to transport water away from

developed areas as quickly as possible. Thus, in some streams in-stream habitat restoration must

occur at time scales commensurate with hydrologic improvement that supports physical habitat

restoration, likely on the order of multiple decades.

For waterbodies impaired due to pollution, attainment of the Stream Biological Objectives shall

not be required until the pollution has been addressed through the implementation measures

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

5

outlined in Section VI.

For waterbodies impaired due to pollutants, the San Diego Water Board may include a

compliance schedule in NPDES permits to achieve the receiving water limitations.

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

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Table TBD: Time Schedule for San Diego Water Board Actions to Implementation of the Stream Biological Objective

Program Area Implementing Party Implementation Action & Compliance Dates General Monitoring and Assessment

Ambient Monitoring San Diego Water Board

1. Monitoring, coordination, and execution of special studies that conduct bioassessment at reference sites and impaired sites in the San Diego Region – Ongoing.

2. Recommend projects related to bioassessment of perennial and seasonal streams for Surface Water Ambient Monitoring Program (SWAMP) funds - ongoing.

Integrated Reporting - 303(d) List/305(b) Report San Diego Water Board

1. For waters where the Stream Biological Objective applies, degradation of biological populations and communities shall be interpreted consistent with the Stream Biological Objective upon the effective date of the Stream Biological Objective.

Education and Outreach San Diego Water Board 1. Beginning within 1 year after the effective date of the Stream Biological Objective.

Planning

Restoration Planning - Total Maximum Daily Loads (TMDLs) and TMDL Alternatives 6

San Diego Water Board

1. Use of the Stream Biological Objective in TMDL and TMDL alternative development will be evaluated following the adoption of the first Integrated Report that incorporates the Stream Biological Objective.

2. Reassessment of restoration planning priorities- ongoing after effective date of Stream Biological Objective.

Permitting

Regional Phase 1 Municipal Separate Storm Sewer System (MS4) NPDES Permit (Phase 1 MS4 Permit)

San Diego Water Board;

Phase 1 MS4 Permittees

1. Within 5 years of the effective date of the Stream Biological Objective, the San Diego Water Board will modify the Phase I MS4 Permit to include implementation requirements to incorporate the CSCI and Stream Biological Objectives. 2. Phase 1 MS4 Dischargers may elect to comply with the Stream Biological Objectives using the “alternative compliance pathway option.” However, 12 months prior to submittal of the ROWD, Phase I MS4 Permittees must notify the San Diego Water Board if they wish to utilize or update an alternative

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

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compliance pathway option to incorporate numeric goals, water quality improvement strategies, and schedules for the Stream Biological Objectives.

Commercial Agricultural Operation Waste Discharge Requirements (WDRS)

San Diego Water Board; 1. Within 5 years of the effective date of the Stream Biological Objective, the San Diego Water Board will revise the Commercial Agricultural WDRs to include conditions (e.g. benchmarks) to implement the Stream Biological Objectives.

CWA § 401 Water Quality Certifications and/or WDRs for discharges of dredged and fill materia

San Diego Water Board; Dredged and fill material dischargers subject to a CWA § 401 certification and/or WDRs

1. For waters where the Stream Biological Objective applies, the San Diego Water Board will require a Receiving Water Biological Assessment on a case-by-case basis upon the effective date of the Stream Biological Objectives.

2. Beginning 2 years after the effective date of the Stream Biological Objectives, the San Diego Water Board will incorporate the CSCI as a performance target for compensatory mitigation where appropriate.

San Diego Water Board Individual NPDES Permits

San Diego Water Board 1. Within 5 years after the effective date of the Stream Biological Objective, the San Diego Water Board will evaluate individual NPDES permits to determine if the discharge is probable threat to the Stream Biological Objective.

2. For discharges found to be a probable threat to the Stream Biological Objective, the San Diego Water Board shall modify, reissue, or adopt a permit with conditions implementing the Stream Biological Objectives as appropriate.

State Water Board General Permits San Diego Water Board 1. Within 5 years of the effective date of the Stream Biological Objective, the San Diego Water Board will evaluate new and existing enrollees to determine if discharges present a probable threat to the Stream Biological Objective.

2. For discharges found to be a probable threat to the Stream Biological Objective, the San Diego Water Board may modify monitoring and reporting requirements or require enrollment in an individual permit as necessary to ensure compliance with the Stream Biological Objective.

San Diego Water Board General Permits

San Diego Water Board 1. Within 5 years after the effective date of the Stream Biological Objective, the San Diego Water Board will evaluate new and existing enrollees to determine if discharges present a probable threat to the Stream Biological Objective.

2. For discharges found to be a probable threat to the Stream Biological Objective, the San Diego Water Board may modify monitoring and reporting requirements or require enrollment in an individual permit as necessary to ensure compliance with the Stream Biological Objective.

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Basin Plan Chapter 4 Framework for Program of Implementation for Biological Objectives

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All other San Diego Water Board Permits and enforcement actions

San Diego Water Board 1. The San Diego Water Board will, as permit renewal opportunities arise and enforcement case are developed, consider implementation of the Stream Biological Objective on a case-by-case basis.

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III.IV. Monitoring and Assessment This section describes the methods and programs that the San Diego Water Board uses to

acquire water quality information on biological condition of perennial and seasonal streams.

Biological monitoring is the best and most efficient evaluation of aquatic life beneficial uses. The

San Diego Water Board assesses perennial and seasonal streams in the San Diego Region for

aquatic life beneficial use attainment using the Stream Biological Objectives as follows:

A. Ambient Monitoring

Assessment of ambient monitoring data is a critical component in the implementation of the

Stream Biological Objectives in planning and permitting programs. In the San Diego Region,

multiple entities conduct stream bioassessment monitoring. These include governmental

agencies, including the San Diego Water Board, regulated dischargers, and non-governmental

organizations. The San Diego Water Board implements bioassessment monitoring in the San

Diego Region through its Surface Water Ambient Monitoring Program (SWAMP). SWAMP

monitoring is independent of permit-related monitoring and seeks to evaluate trends in water

quality throughout the San Diego Region. The inclusion of ambient monitoring by the San Diego

Water Board specific to biological objectives will be in the San Diego Water Board SWAMP 3-year

contract following biological objectives approval. Dischargers into perennial and seasonal

streams may also be required to conduct bioassessment under a discharge permit or as part of

an enforcement action. This bioassessment data is reviewed by San Diego Water Board staff to

determine compliance with water quality objectives, evaluate efficacy of best management

practices, tailor appropriate discharge requirements, and assess corrective action. Biological

monitoring and assessment, when required or conducted by the San Diego Water Board, will be

done in surface waters in conjunction with chemical and physical measurements of receiving

waters and, where applicable, of discharges.

B. Integrated Reporting

The Federal Clean Water Act (CWA) requires that California report on the quality of its surface

waters every two years. The 305(b) Report assigns an Integrated Report Condition Category to

all assessed water segments. The 303(d) List compiles water segments that do not meet, or are

not expected to meet, applicable water quality standards by the next listing cycle. Together, these

lists make-up the California Integrated Report (Integrated Report).

Development of the Integrated Report is the result of a collaborative process between the State

and Regional Water Boards. The Water Quality Control Policy for Developing California’s Clean

Water Act Section 303(d) List (Listing Policy) describes the requirements for evaluating waters

placed on the Section 303(d) List. In California, water segments may be placed on the 303(d) List

for significant degradation in biological populations and/or communities if the degradation is

associated with a pollutant (e.g. toxicants, temperature, dissolved oxygen, sediment). The

relationship between the Listing Policy and the Stream Biological Objectives is as follows:

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• For water segments where the Stream Biological Objective applies, a water segment

may be placed on the 303(d) List if the water segment’s CSCI score is less than the 10th

percentile of reference calibration sites and this CSCI score is associated with a pollutant.

Association with a pollutant is determined using the applicable sections of the Listing

Policy, including but not limited to sections: 3.1, 3.2, 3.6, 3.7, and 6.1.5.9.

• For water segments where the Stream Biological Objective applies but no CSCI data is available, or if the CSCI data is inappropriate due to natural conditions, a

water segment will continue to be placed on the 303(d) list in accordance with section 3.9

of the Listing Policy or other applicable sections.

• For water segments where there are no applicable biological objectives,

assessment for placement on the 303(d) list will be conducted in accordance with the

Listing Policy.

Where a water segment is impaired due to pollution, the San Diego Water Board will place the

water segment into Category 4C (impaired due to pollution, no TMDL required). Waterbodies

placed into Category 4C for will not be placed in other categories for biointegrity impairments until

the pollution impairment is addressed. When a water segment is impaired only due to a

pollutant(s), the San Diego Water Board will place the water segment into one of the following

Integrated Report categories: Category 5 (TMDL still required), Category 5-Alt (being addressed

by action other than a TMDL), Category 4A (being addressed by approved TMDL), Category 4B

(being addressed by EPA approved alternative restoration approach). Where a water segment is

impaired due to pollution,9 the San Diego Water Board will place the water segment into Category

4C (impaired due to pollution, no TMDL required). The San Diego Water Board may use rapid

causal assessment methods for water segment assessment, as well as for evaluating a water

segment’s recovery potential, developing timeframe(s) for potential restoration targets, and

selecting potential restoration methods and mitigation measures. The number and type of

potentially associated impairment sources will be utilized for San Diego Water Board TMDL

prioritization in the Integrated Report (see Section IV, Planning).

Water segments will be removed from the section 303(d) list, if data demonstrates the Stream

Biological Objective listing thresholds are not exceeded over the duration of the listing cycle or

there are no longer associated pollutants applicable to the Stream Biological Objective

impairment.

C. Education and Outreach

A critical component of monitoring and assessment efforts includes the sharing of bioassessment

data with the public. Bioassessment data collected by the San Diego Water Board and required to

be collected by regulated parties is publicly available data. Currently the San Diego Water Board

uploads data it collects into the California Environmental Data Exchange Network (CEDEN), a

publicly accessible database. The San Diego Water Board will also use education and outreach

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efforts to convey these results to the public. Such efforts include but are not limited to:

development of watershed status sheets and/or San Diego Water Board informational items,

presentations at conferences or stakeholder meetings, and participation in public events.

IV.V. Planning This section describes how the San Diego Water Board will incorporate water quality information

on biological condition of perennial and seasonal streams into its water resource planning and

decision making. The San Diego Water Board uses the planning process for the protection and

restoration of waters meeting or not meeting water quality objectives. The planning process

includes Regional Board initiatives such as the Basin Plan Triennial Review, TMDL and Basin

Plan amendments, non-point source management planning, and the development and

implementation of the Integrated Report.

Evaluation of the biological condition of waterbodies is critical to guide and prioritize appropriate

planning implementation actions. Adoption of the Stream Biological Objectives enables the San

Diego Water Board to co-evaluate stream physical habitat and hydrology, in addition to chemical

water quality objectives. Assessment of physical habitat and hydrology will include metrics such

as duration, magnitude, variability and frequency for hydrology and flow habitat, substrate type,

riparian cover and channel cover for habitat. Other physical habitat and hydrologic metrics may

be evaluated as appropriate given site and landscape characteristics. Combining the evaluation

of physical and chemical components of stream integrity when implementing planning programs

is expected to result in successful protection and meaningful restoration of beneficial uses in

perennial and seasonal streams as described below.

A. TMDLs and other Actions to Restore Impaired Waters

The Water Quality Control Policy For Addressing Impaired Waters: Regulatory Structure and

Options (Impaired Waters Policy) provides guidelines for developing and implementing TMDLs

and water board TMDL programs. The San Diego Water Board determines the appropriate

regulatory and/or non-regulatory actions to attain water quality objectives and restore aquatic life

beneficial uses consistent with the Impaired Waters Policy. Adoption of a Stream Biological

Objective does not affect implementation of the Impaired Waters Policy. Instead, the Stream

Biological Objective provides clarity in determining the appropriate regulatory and/or non-

regulatory actions to attain water quality objectives and restore aquatic life beneficial uses

consistent with the Impaired Waters Policy.

i. Using the Stream Biological Objective to Guide TMDL and Alternative Restoration Strategy Development

The San Diego Water Board will use available data and information on biological condition to

guide the selection and development of appropriate strategies for restoring impaired waters. The

monitoring and assessment process will be used to identify streams that are meeting or not

meeting the Stream Biological Objective (see Section III, Monitoring and Reporting). Where the

Stream Biological Objectives are not met in a receiving water, the San Diego Water Board will

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conduct an causal assessment of chemical and physical data will be conducted to determine the

cause and associated sources of the impaired condition. Causal identification will use an

approach based on using comparable reference and impacted sites, combined with the best

available causal assessment science. The San Diego Water Board may also use the USEPA's

Causal Analysis/Diagnosis Decision Information System (CADDIS) where appropriate. The San

Diego Water Board has discretion when determining how to address impaired waters consistent

with the Impaired Waters Policy. In most case, the San Diego Water Board will use one, or a

combination of, the following tools and mechanisms to address biological impairments:

• If data shows the impairment is due to nonpoint sources, the San Diego Water Board will

prioritize inclusion of the Stream Biological Objectives as a regional initiative in the

California nonpoint source program implementation plan.

• If data shows the impairment is not associated with the discharge of a pollutant (i.e.

physical habitat and/or hydrologic impairment only), the San Diego Water Board will

consider non-TMDL approaches to address the impairment, including consideration of

Use Attainability Analyses and site-specific objectives.

If data shows that impairment is associated with a chemical pollutant(s), development of a TMDL

or TMDL Alternative will be required to address the pollutant(s) causing or contributing to the

impaired condition.

Biological condition metrics also provide an opportunity for the San Diego Water Board to identify

when a TMDL or TMDL Alternative will result in restoration of biological integrity within a

meaningful timeframe given the physical condition of the waterbody. The San Diego Water Board

will mayuse the Stream Biological Objective to establish a minimum restoration goal or target for

the TMDL and TMDL Alternatives in water segments where the Stream Biological Objective

applies. The San Diego Water Board will consider the physical sources contributing to the

impairment (e.g. habitat modification) in order to guide and prioritize the selection of waterbodies

for TMDL or alternative restoration strategies. For waterbodies where impairments of example,

using the Stream Biological Objective are partially caused by pollution, TMDLs to address

pollutants contributing to impairments of the Stream Biological Objective may will be determined

to be a lower priority in low elevation concrete-lined streams, as the physical habitat

modificationpollution would need to be addressed first for beneficial use restoration, and such

restoration may require a longer time scale than that used in TMDL implementation to address

pollutants.

ii. Using the Stream Biological Objective to Review Existing Water Quality Objectives

The planning process is expected to identify the specific levels of pollutants that are causing or

contributing to a Stream Biological Objective impairment. The San Diego Water Board intends to

use this information to set load and/or concentration-based requirements at the levels necessary

to restore biological condition. This process may also identify chemical water quality objectives in

the Basin Plan that need to be modified. As a result, the San Diego Water Board expects

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adoption of the Stream Biological Objectives could result in the review and/or revision of existing

chemical water quality standards to better represent site-specific conditions that are protective of

beneficial uses. Any revisions of a water quality standard would require a Basin Plan amendment

iii. Using the Stream Biological Objective for Protection Planning

State Water Board Resolution No. 68-16 requires the maintenance of the existing high quality of

water unless a change in water quality “will be consistent with maximum benefit to the people of

the State…” The San Diego Water Board will consider waters in compliance with the Stream

Biological Objectives (i.e. waters with reference or near-reference condition) as high-quality

waters subject to protection (See Section VII, Antidegradation Policy), and such waters will be

considered a high priority during the San Diego Water Board’s planning process.

V.VI. Permitting This section describes how the San Diego Water Board will incorporate the Stream Biological

Objective into its permitting program. The Stream Biological Objective is established for the

protection of aquatic life beneficial uses applicable to perennial and seasonal streams (See Table

2-2, Beneficial Uses of Inland Surface Waters). The San Diego Water Board will use its permitting

authorities to ensure that any authorized discharge does not prevent attainment of the Stream

Biological Objective.

a. Applicability of the Stream Biological Objective

The Stream Biological Objective applies to all perennial and seasonal streams in the San Diego

Region.

b. Standard Implementation Requirements

The Stream Biological Objective shall be incorporated into NPDES permits issued pursuant to

CWA section 402, WDRs issued pursuant to California Water Code (CWC) section 13263,

waivers of WDRs issued pursuant to CWC section 13269, and water quality certifications issued

pursuant to CWA section 401 as follows:

A. Phase I Municipal Separate Storm Sewer Systems (MS4) Dischargers

Pollutants from municipal runoff are regulated through the NPDES Storm Water Program. CWA

section 402 establishes the NPDES Program to regulate the ‘‘discharge of a pollutant,’’ other than

dredged or fill materials, from a ‘‘point source’’ into ‘‘waters of the U.S.” (CWA §§ 1342(a) &

1362(12)). CWA section 402(p) requires pollutants in storm water discharges to be reduced using

a combination of source control and, if necessary, treatment practices that are selected based

consideration of the characteristics of the discharge and receiving water. Pollutants in municipal

(MS4) storm water discharges must be reduced to the maximum extent practicable (MEP).

Phase 1 MS4 Dischargers enrolled under the regional Phase 1 MS4 are required to develop and

implement programs and plans using an adaptative management framework to select and

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address the highest priority water quality issues in their watershed.

i. Phase I MS4 Permit Conditions

To implement the Stream Biological Objective, the San Diego Water Board will revise the Phase I

MS4 Permit to update provisions related to programs and plans as follows:

Phase I MS4 Dischargers shall be required to:

• consider the biological condition of the receiving water when identifying priority water

quality conditions in each watershed. This consideration shall include an assessment of

the receiving water’s combined physical, chemical, and biological condition relative to

storm water and non-storm water discharges.

The incorporation of Stream Biological Objective assessment in the WQIP process does not

preclude Phase I MS4 dischargers from choosing other water quality conditions (e.g. human

health, chemical pollutant impairments) as the highest priority water quality conditions in the

watershed. However, CSCI scores, where applicable, should be used to guide selection and

implementation of water quality improvement strategies to address high priority water quality

conditions impacting the biological condition of the receiving water. Phase I MS4 Dischargers

may also use CSCI scores to prioritize implementation actions. For example, a Phase I MS4

Discharger could target structural and nonstructural strategies that protect or restore aquatic life

beneficial uses using the following preference hierarchy (for example purposes):

• Protect high quality sites that meet or exceed the Stream Biological Objective.

• Protect sites that meet the Stream Biological Objective but are vulnerable.

• Restore sites that do not meet the Stream Biological Objective.

If biological conditions in streams are identified as a high priority condition in the watershed, all

elements relating to the Stream Biological Objective must be updated pursuant in the applicable

required watershed management plan17

pursuant to the reporting requirements of the Phase I

MS4 Permit.

ii. Phase I MS4 Monitoring and Assessment Requirements The Stream Biological Objective shall be assessed as part of the Monitoring and Reporting

Program in the Phase I MS4 permit at locations representative of the discharge. If the Stream

Biological Objective is not attained in the receiving water, the Discharger shall complete further

investigation to identify if the non-attainment is a result of pollutants discharged from the MS4.

The evaluation will be conducted as described in section V.A.3, Process for Conducting a Biological Objective Evaluation, below. The San Diego Water Board may waive a

Biological Objective Evaluation if monitoring and assessment data indicates that an external

factor, unrelated to a discharge, is causing or contributing to the low CSCI score.

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iii. Process for Conducting a Biological Objective Evaluation

The Biological Objective Evaluation will use receiving water data, site monitoring data, and

discharge data together to evaluate whether pollutant(s) in a MS4 discharge is causing or

contributing to nonattainment of the Stream Biological Objective. Determination of if a discharge

causes or contributes to degradation will consider the pollutants, magnitude, and duration of the

discharge in relation to the physical, chemical and biological condition of the receiving water. In

many cases, there may be physical constraints, historic discharges (e.g. stream fill) or land use

practices that have directly caused existing degraded biological conditions in receiving waters

that are not caused by the discharge.

At a minimum, a Biological Objective Evaluation shall include:

• an evaluation of the monitoring data of chemical and physical characteristics of the

discharge, and an evaluation of the upstream and downstream receiving water

conditions, including physical and chemical conditions.

• a description of actual or suspected factors causing or contributing to the observed

condition, including any regulated or illicit discharge of the permittee and/or external

factors.16

• if a regulated or illicit discharge of the permittee is a suspected or actual

stressor,discussion of additional or improved best management practices to prevent or

minimize,the discharges of waste that may be causing or contributing to the observed

condition.

• If the identified cause of the lowered CSCI scores is determined to be pollution and not

pollutants, the permittees may include voluntary in-stream habitat restoration should such

actions be deemed suitable and feasible by the permittee(s) on a site-specific basis, but

identification of additional or improved best management practices is not required.

iv. Compliance Determination

The Phase 1 MS4 Permit shall include the permit conditions, Monitoring and Reporting and

Biological Objective Evaluation requirements in V.A.1-3. The Phase 1 MS4 Permit should include

compliance language stating that MS4s are only responsible for addressing pollutants causing or

contributing to lowered CSCI scores to the Maximum Extent Practicable. The Phase 1 MS4

Permit conditions should clarify that implementation of the permit requirements, including

the best management practices identified as part of the Biological Objective Evaluation will

constitute compliance with any conditions resulting from the Stream Biological Objectives.

The Stream Biological Objective shall not be utilized on its own as a receiving water limitation or

translated into or applied as effluent limitations. Pollutants identified through a causal

assessment as causing or contributing to the nonattainment of the Stream Biological Objective

may be included as receiving water limitations as needed, but shall not be translated into effluent

limitations.

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B. Agricultural Dischargers

Commercial Agricultural Dischargers in the San Diego Region are required to enroll in WDRs.

These WDRs require enrollees to implement best management practices and conduct monitoring

and reporting. To implement the Stream Biological Objective, the San Diego Water Board will

revise the Waste Discharge Requirements to include a water quality benchmark for the Stream

Biological Objective and include bioassessment in the Monitoring and Reporting Program at its

discretion.

C. All Other Permittees

i. Permit Application Requirements

a. 1Determining Whether an Application to Discharge Requires Submission of a Receiving Water Biological Assessment

CWC section 13260 requires any person discharging or proposing to discharge waste that could

affect the quality of the waters of the state, other than into a community sewer system, to file a

Report of Waste Discharge (ROWD). Submission of a ROWD starts the application process for

issuance of a permit issued by the San Diego Water Board except where the ROWD is waived.

The San Diego Water Board will require new and existing discharge applicants to submit a

technical report that characterizes the biological condition of the receiving water(s) (Receiving

Water Biological Assessment) as part of a ROWD, if the applicant meets one of the following

requirements:

• the discharge is to a seasonal stream, and

• the discharge duration is greater than 2 months, and

• the discharge is outside of the rainy season (Oct. 1st to May 30

th); or

• the discharge is to a high-quality10

waterbody.

This ROWD requirement under this section are not applicable for Phase I MS4 or Agricultural

dischargers, as special implementation requirements apply (see Section VI below). For

discharges where there is an alternative application form to discharge (e.g. Notices of Intent to

enroll in a general permit, waivers of WDRs, or 401 certification application), the San Diego Water

Board will require a Receiving Water Biological Assessment on a case-by-case basis. The San

Diego Water Board may also require submittal of a Receiving Water Biological Assessment if a

discharge is proposed for a receiving water that possesses unique, uncommon, or

environmentally sensitive biological characteristics.

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b. 2Contents of a Receiving Water Biological Assessment12

At a minimum, the Receiving Water Biological Assessment must include:

• Discussion of the existing biological condition of the receiving water(s). This discussion

should include CSCI scores if known. Where no CSCI scores are available, the San

Diego Water Board may require the collection of data for CSCI scores, on a case-by-case

basis.

• Discussion of potential temporary or permanent impacts to the biological condition of the

receiving water from the discharge. This discussion should be supported by evidence.13

Discussion of whether flow from the discharge will cause or contribute to a condition of

erosion. This discussion should include an evaluation of the need for engineered stream

channel modifications and identify erosion mitigation measures associated with the

discharge and receiving water.

• Discussion of whether the discharge has the potential to cause a reduction in the

biological condition in the receiving water via changes to hydrologic, physical, or chemical

characteristics of the receiving water. This discussion should evaluate a decrease in the

receiving water’s CSCI score (if known).

• Discussion of any natural or background conditions that may affect the receiving’s

• water’s CSCI score (if known).

• Proposed best management practices to protect receiving water condition.

• Proposed discharges to high-quality waters must also include:

o Discussion of baseline biological condition of the receiving water. Baseline water

quality is the best water quality achieved since [Effective Date].

o Discussion of past, present, and probable beneficial uses of the receiving water.

o Discussion of the estimated severity and extent of water quality reduction as a result

of the discharge.

o Discussion of any public benefit associated with the discharge (e.g. economic or

social development).

o Discussion of negative economic or social costs associated with the discharge (e.g.

increased taxes, decreased land value, loss of unique environmental resources, etc.)

o Discussion of a range of practicable discharge alternatives to reduce, eliminate, or

compensate for negative impacts to the biological condition of the receiving water.

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iv.ii. Permit Requirements

a. 1Establishing Discharge Limits for the Stream Biological Objective

The Stream Biological Objective shall apply as a receiving water limit. The Stream Biological

Objective shall not be translated into or applied as an effluent limitation unless the following

conditions are met:

• A clear causal relationship has been established linking the discharge and nonattainment

of the Stream Biological Objective,

• The pollutants or physical factors causing or contributing to nonattainment of the Stream

Biological Objective have been identified, and

• Loading studies have been completed to estimate the reductions in pollutant loading for

the discharge that will restore the beneficial use(s).

b. 2Determining if a Discharge is a Probable Threat

The San Diego Water Board shall incorporate appropriate permit requirements14

to implement the

Stream Biological Objective for any discharge that is a probable threat to the Stream Biological

Objective.

A discharge is considered a probable threat to the Stream Biological Objective if the discharge is

or has the potential to cause or contribute to a decrease in the CSCI score in the receiving water

or downstream waters as identified in the ROWD or determined by the San Diego Water Board. If

there is no CSCI score for a receiving water or the use of a CSCI score is inappropriate due to

natural conditions, the San Diego Water Board will determine probable threat on a case-by-case

basis. In making this determination, the San Diego Water Board will consider the magnitude,

duration, and composition of the discharge, as well as the physical, chemical, and biological

conditions of the receiving water and immediate downstream waters.

c. 3Minimum Permit Requirements for Discharges that Pose a Probable Threat to the Stream Biological Objective

Discharge limits and best management practices designed to meet chemical and physical water

quality objectives are expected, in many cases, to be protective of the Stream Biological

Objectives. Permit requirements will be based upon a determination of whether the biological

condition is associated with the discharge or non-discharge factors (non-discharge factors include

but are not limited to: in-stream channel modification, habitat modification, upstream discharges

or diversions). At a minimum, the San Diego Water Board shall include waste discharge

requirements that address any toxicity, hydrology, and nutrient related impacts to the receiving

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water unless the biological condition is solely a result of non-discharge factors. The San Diego

Water Board may impose additional permit requirements to treat or control discharges that affect,

or have the potential to affect, the biological condition of the receiving water. For example, where

nutrient related stressors are causing or contributing to nonattainment of the Stream Biological

Objective, the San Diego Water Board may require enhanced nutrient removal in the discharge.

d. 4Minimum Monitoring and Assessment for Discharges with Stream Biological Objective Permit Conditions

Monitoring and assessment programs in permits where the Stream Biological Objective is applied

as a discharge limitation (i.e. a receiving water limit or effluent limit) will be used to assess

compliance with the discharge limitation and to monitor effectiveness of best management

practices. Bioassessment will be required in all permits where the discharge is a probable threat

to the attainment of the Stream Biological Objective (Section V.B.2) or where a clear causal

relationship has been established linking the discharge and nonattainment of the Stream

Biological Objective (Section V.B.1).

Monitoring may be performed by individual permittees, through participation in a group monitoring

coalition, or a combination of individual and group monitoring. For permit renewals, the San Diego

Water Board will evaluate prior monitoring requirements to determine if these requirements can

be reduced to off-set new costs associated with bioassessment.

Monitoring and assessment programs shall be designed to meet the following minimum

requirements:

• Bioassessment shall be conducted at location(s) representative of the discharge(s) and

at a comparator site uninfluenced by the discharge(s) (typically upstream).

• Samples and measurements taken for the purposes of bioassessment shall be

representative of the volume and nature of the discharge.

• Bioassessment shall be conducted according to the methodology in the Standard

Operating Procedures (SOPs) for the Collection of Field Data for Bioassessments of

California Wadeable Stream: Benthic Macroinvertebrates, Algae, and Physical Habitat15

unless another bioassessment method is specified by the San Diego Water Board. The

San Diego Water Board may approve equivalent bioassessment procedures at its

discretion.

• Bioassessment must include sampling for the taxonomic analysis of benthic

macroinvertebrate (BMI) assemblages, stream physical habitat data, and water

chemistry.

• Water chemistry sampling must include sampling for turbidity (NTU), temperature (°C),

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specific conductivity (µS/cm), salinity (ppt), alkalinity (mg/L), pH, and dissolved oxygen

(mg/L and % saturation).

• Bioassessment shall be conducted at a frequency of no less than once per permit term.

• Discharges identified as causing or contributing to an exceedance of the Stream

Biological Objective must be evaluated more frequently.

The San Diego Water Board may require additional monitoring (e.g. water chemistry, toxicity,

algae) on a case-by-case basis. When requiring additional monitoring, the San Diego Water

Board shall consider the nature of permitted activity, constituent(s) of concern associated with the

discharge, and the condition of the receiving water.

The San Diego Water Board will determine compliance with permit conditions established based

on the the Stream Biological Objective using a “comparator site” approach. Under a comparator

site approach, the San Diego Water Board compares the biological condition of the receiving

water subject to the discharge to a site uninfluenced by the discharge. In most cases, the San

Diego Water Board will compare the CSCI scores at a monitoring site downstream of the

discharge relative to a comparative monitoring site (typically upstream). Where the San Diego

Water Board has determined that the CSCI is inappropriate due to natural conditions, the San

Diego Water Board will consider alternative evidence of biological condition (e.g. Algal Index of

Biotic Integrity for Southern California Streams” scores, “California Rapid Assessment Method”

(CRAM) scores, and sediment or water chemistry) and this section does not apply.

c.e. 1Determining When There is an Exceedance of a Permit Condition Established Based on the Stream Biological Objective

An exceedance of the Permit Condition established based on the Stream Biological Objective is

demonstrated when:

• the CSCI score is less than the 10th percentile threshold in Chapter 3 of this Basin

Plan;and

• the San Diego Water Board or the Discharger determine that the discharge is causing or

contributing to the low CSCI score.

d.f. 2Determining When Further Investigation of a Potential Exceedance is Required

If the CSCI score is less than the 10th

percentile threshold, the Discharger shall complete further

investigation to verify impacts to the biological condition in the receiving water and to evaluate the

potential stressors contributing to the low CSCI score as described in section V.C.3.c, Process for

Conducting a Biological Objective Evaluation, below. The San Diego Water Board may waive a

Biological Objective Evaluation if monitoring and assessment data indicates that an external

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factor, unrelated to a discharge, is causing or contributing to the low CSCI score.

e.g. 3Process for Conducting a Biological Objective Evaluation

The Biological Objective Evaluation will use receiving water data, site monitoring data, and

discharge data together to evaluate whether a discharge is causing or contributing to

nonattainment of the Stream Biological Objective and to provide active feedback on the efficacy

of permit implementation.

At a minimum, a Biological Objective Evaluation shall include:

• an evaluation of the monitoring data of chemical and physical characteristics of the

discharge, and

• an evaluation of the upstream and downstream receiving water conditions, including

physical and chemical conditions.

• a description of actual or suspected factors causing or contributing to the observed

condition, including any regulated or illicit discharge of the permittee and/or external

factors.16

• a description of best management practices currently being implemented and their

effectiveness, and

• if a regulated or illicit discharge of the permittee is a suspected or actual stressor,

discussion of additional or improved best management practices to prevent or minimize

the discharges of waste that may be causing or contributing to the observed condition.

C.D. CDischargers of Dredged and Fill Material

The San Diego Water Board’s Dredge, Fill, and Wetlands Program regulates all discharges of

dredged and fill material to Waters of the State,18

but has special responsibility for wetlands,

riparian areas, and headwaters because these waterbodies have high resource value, are

vulnerable to filling, and are not systematically protected by other programs. For discharges of

dredged and/or fill material to waters of the State where the Stream Biological Objective applies,

CSCI scores may be used, on a case-by-case basis to evaluate avoidance and minimization of

direct, indirect, and cumulative impacts from the discharge, to set performance standard(s) for

restoration of temporally impacted aquatic life beneficial uses, and to determine successful

compensatory mitigation for permanent loss of aquatic life beneficial uses.

VII. Waterbodies with Pollution as a Contributing Cause of Nonattainment of the Biological Objectives

For those waterbodies where pollution, such as in-stream channel hardening, already cause

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and/or contribute to an exceedance, permitted dischargers are not required to remedy existing

instream physical habitat condition unless a condition of proposed mitigation associated with a

site-specific project, or as a matter of enforcement (e.g. illegal fill). Instead, the discharger would

be, consistent with existing water quality objectives, required to ensure its discharge does not

contribute to the continued degradation or increase the level of degradation, resulting in additional

Beneficial Use loss.

Nonattainment of Biological Objectives due to pollution will be addressed through enforcement

actions, voluntary permit actions, and nonregulatory actions, but will not be included as required

permit conditions.

VI.

VII.VIII. Antidegradation Policy Any action that may result in a lowering of water quality must satisfy applicable requirements in

the Federal and State antidegradation policies set forth in 40 C.F.R. section 131.12 (Federal

Antidegradation Policy) and State Water Board Resolution No. 68-16, Statement of Policy with

Respect to Maintaining High Quality Waters in California (State Antidegradation Policy)

(collectively Antidegradation Policies). In general, the Antidegradation Policies require that the

existing water quality be maintained unless the San Diego Water Board makes sufficient findings

to justify a lowering of water quality (See Chapter 3 and Chapter 5 of the Basin Plan).

The San Diego Water Board applies the Antidegradation Policies on a parameter-by-parameter

basis. The San Diego Water Board therefore will consider the potential for degradation of the

Stream Biological Objective separately from other parameters when approving any action with the

potential to adversely affect the biological condition of a perennial or seasonal stream.

The extent of biological condition information required to support an antidegradation analysis will

depend on the specific conditions of the discharge. Administrative Procedures Update 90- 004,

(application of antidegradation requirements in NPDES Permitting), State Water Board Order WQ

2015-0075 (application of antidegradation requirements to stormwater discharges) and State

Water Board Order WQ 2018-0002 (application of antidegradation requirements to nonpoint

source discharges) provide guidance for the regional boards on the level of detail needed to

support an antidegradation analysis in certain regulatory contexts. The San Diego Water Board

will continue to use this guidance as appropriate. In some instances, use of best professional

judgment and limited biological condition information may be sufficient to determine that a

perennial and seasonal stream will not be degraded. If additional information on the biological

condition is needed to evaluate compliance with the Antidegradation Policies, the San Diego

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Water Board may require a discharger to submit supplemental information on the biological

condition of a receiving water as part of a Report of Waste Discharge (See section V.A.2,

Contents of a Receiving Water Biological Assessment), or other technical report pursuant to CWC

Sections 13267 or 13383.

The Antidegradation Policies will be implemented as described below.

A. Federal Antidegradation Policy

The Federal Antidegradation Policy is triggered by a reduction in water quality in a Water of the

United States. If a perennial or seasonal stream meets the federal definition for Waters of the

United States in 40 CFR 230.3(s), compliance with the Federal Antidegradation Policy would

require consideration of the following factors as set forth in 40 C.F.R. § 131.12(a)(1-2):

• the existing water quality is adequate to achieve and maintain compliance with existing

instream uses.

• if the baseline quality of a waterbody “exceeds levels necessary to support propagation of

fish, shellfish, and wildlife and recreation in and on the water, that quality shall be

maintained and protected” unless the San Diego Water Board makes findings that (1) any

lowering is necessary to accommodate important economic or social development in the

area in which the waters are located; (2) water quality adequate to protect existing uses

is fully assured; and (3) “the highest statutory and regulatory requirements for all new and

existing point sources and all cost-effective and reasonable best management practices

for nonpoint source control”.

This provision has been interpreted to mean that, “[i]f baseline water quality is equal to or less

than the quality as defined by the water quality objective, water quality shall be maintained or

improved to a level that achieves the objectives.” (See State Water Board, Administrative

Procedures Update, Antidegradation Policy Implementation for NPDES Permitting, 90-004 (APU

90-004), p. 4.) Therefore, in evaluating, whether existing water quality is adequate to achieve and

maintain compliance with aquatic life beneficial uses, the San Diego Water Board will look at

CSCI scores.

B. State Antidegradation Policy

The State Antidegradation Policy is triggered by a reduction in water quality in a Water of the

United of the State that is considered “high quality.” If the baseline21

water quality in a perennial

or seasonal stream exceeds the water quality necessary to achieve compliance with the Stream

Biological Objective, then the San Diego Water Board may not authorize degradation of the water

quality unless it finds (1) that the degradation is consistent with the maximum benefit of the

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people of the state, (2) will not affect a water’s present and anticipated beneficial uses, (3) will not

result in water quality less than that prescribed in policies (i.e. lower than the Stream Biological

Objective), and (4) will ensure the best practicable treatment or control (BPTC) of discharges.

For the purposes of the State Antidegradation Policy, a perennial or seasonal Stream with a

baseline biological condition that is attaining reference conditions is considered “high quality”.

Perennial and seasonal streams with a CSCI score greater than or equal to the 10th

Percentile of

the CSCI scores are attaining reference conditions.

The San Diego Water Board will evaluate whether there is a potential for a reduction in water

quality by considering the potential for the discharge to cause a decrease in the CSCI score. A

decrease occurs when a CSCI score(s) is lower than the expected inter-annual variability

observed at similar reference sites. The San Diego Water Board recognizes that CSCI data is not

always available for a given receiving water. In the absence of CSCI data, the San Diego Water

Board will use best professional judgement to determine existing and baseline biological condition

of the receiving water using all available and relevant information, including but not limited to

CRAM scores, IBI scores for algae, IBI scores for benthic macroinvertebrates, or water and

sediment chemistry data.

VIII.IX. Compliance Assurance The San Diego Water Board staff will ensure perennial and seasonal streams are meeting the

Stream Biological Objectives though regular inspections of receiving waters, collection of

biological data, review of discharger monitoring reports, and the review and analysis of other

relevant data.

Where Stream Biological Objectives are not achieved, the San Diego Water Board will review

compliance with relevant permits that discharge to the receiving water and review assessments

from dischargers and other sources. The San Diego Water Board may assess compliance based

on existing information or use discretionary authority to require other parties to provide data or

information (e.g. CWC Sections 13225, 13267, 13383). ¶

IX.X. Enforcement The CWC authorizes the San Diego Water Board to enforces water quality laws, regulations, and

plans to protect waters of the state (see e.g. CWC §§ 13304, 13350 and 13385). If the San Diego

Water Board determines that there is a violation of the Stream Biological Objective, it will take

progressive enforcement as outlined in the State Water Board’s 2017 Enforcement Policy, or

future amendments to this Policy. Where sufficient data exists, the San Diego Water Board will

use Stream Biological Objective data in the penalty liability calculation process to assess the

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harm or potential harm to aquatic life beneficial uses for alleged discharge and non-discharge

violation(s) relating to perennial and seasonal streams. The discharger may also be required to

collect biological, chemical, and physical water quality monitoring data in order to make a

potential for harm determination at the San Diego Water Board’s discretion.

For enforcement actions that involve injunctive terms (e.g. a Cleanup and Abatement Order,

Cease and Desist Order, Time Schedule Order) or an alternative to civil liability assessment (e.g.

a compliance project, supplemental environmental project, enhanced compliance action), the San

Diego Water Board will use Stream Biological Objective data as an evaluative and success

measure where appropriate, including but not limited to: establishment of compliance milestones,

determination of cleanup targets and goals, and development of compliance monitoring.

X.XI. Financial Assistance The State Water Board’s Division of Financial Assistance (DFA) administers financial assistance

programs that include loans and grants for constructing municipal sewage and water recycling

facilities, remediation for underground storage tank releases, watershed protection projects, and

for nonpoint source pollution control projects, etc. The San Diego Water may evaluate

prospective projects for financial assistance and administers these grants and loans as contract

managers. For San Diego Water Board administered environmental projects and grants that

target aquatic-life beneficial uses, Stream Biological Objective data may be required on a case-

by-case basis to establish performance milestones and metrics. The San Diego Water Board may

also use Stream Biological Objective data to evaluate Cleanup and Abatement Account requests

for funding projects in key areas, as identified by the San Diego Water Board, specifically for

projects that focus on the restoration of degraded habitat and/or protection of ecosystem health.

XI.XII. Development of Future Biological Objectives In the San Diego Region there are surface waters other than perennial and seasonal streams

that have aquatic-life beneficial uses. The San Diego Water Board may develop future biological

objectives on a categorical or waterbody specific basis as additional science-based biological

integrity metrics or indices are developed or in response to periodic Basin Plan reviews. Future

biological objectives shall be developed using the following guidance:

• Surface waters within the San Diego Region shall support an ecologically balanced and

resilient community of organisms having a native species composition, abundance, and

functional organization commensurate with that of unaltered analogous waters.

• Biological Integrity metrics or indices use to translate or develop a biological objective

shall, to the greatest extent feasible, meet the following minimum requirements:

o be USEPA Level 3 quantitative assessments;

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o be published in a scientifically peer-reviewed journal;

o be specific to waterbodies or waterbody types; and

o be repeatable using standardized operating procedures.

See Figure TBD for a flow chart of the typical development process for development of biological

integrity metrics or indices:

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¶

Figure TBD. Biological Integrity Metric Development Steps