Water Quality Improvement Plan Provision B.2 Submittal: Priority Water Quality Conditions

Transcription

1 JUNE 2017 [ REVISED DRAFT] SANTA MARGARITA RIVER WATERSHED MANAGEMENT AREA Water Quality Improvement Plan Provision B.2 Submittal: Priority Water Quality Conditions Submitted by COUNTY OF RIVERSIDE, COUNTY OF SAN DIEGO, RIVERSIDE COUNTY FLOOD CONTROL AND WATER CONSERVATION DISTRICT, CITIES OF MENIFEE, MURRIETA, TEMECULA, WILDOMAR Prepared by LARRY WALKER ASSOCIATES GEOSYNTEC CONSULTANTS

2 Table of Contents 2 Priority Water Quality Conditions Process to Prioritize Water Quality Conditions Data Received and Analyzed Step 1A. Impaired Receiving Waters and Total Maximum Daily Loads (Provisions B.2.a.(1) and B.2.a.(2)) Step 1A. 303(d) Listings Step 1A. TMDLs Step 1B. Evaluation of Continued Exceedances and Trends Step 2. Identify Significant Regulatory Actions Step 3. Assess Potential Beneficial use Impacts Beneficial Uses in the SMR Subareas Location of Known Beneficial Uses and Sensitive Receiving Waters Results of Assessment of Potential Beneficial Use Impacts Step 4. Assessment of Potential MS4 Impacts (Provision B.2.b) Assessment of MS4 Discharges Priority Water Quality Conditions Priority Water Quality Conditions (Provisions B.2.c.(1)(a-d)) Monitoring Data Adequacy and Data Gaps (Provision B.2.c.(1)(e)) Step 5B. Highest Priority Water quality Condition (Provision B.2.c.(2)) Identification of MS4 Sources of Pollutants and/or Stressors Potential Water Quality Improvement Strategies Santa Margarita River WMA i June 2017 Water Quality Improvement Plan [FINAL DRAFT]

3 List of Figures Figure 2-1. Priority Condition Assessment Subareas Figure 2-2. Prioritization Process for the SMR WMA Figure 2-3. Dry Weather Water Quality Objective and Threshold Exceedances in SMR WMA Figure 2-4. Wet Weather Water Quality Objective and Threshold Exceedances in SMR WMA Figure 2-5. SMR Sensitive Waters Wetlands Defined by the NWI and Cole Creek with BIOL Beneficial Use Figure 2-6. Upper SMR Subwatershed Channel Characteristics and Areas Identified by Consultation Committee for Investigation Figure 2-7. Reaches, Major Outfalls with Tributary Areas, and Outfall Monitoring Locations within the Upper Santa Margarita River Subwatershed Figure 2-8. Outfall Monitoring Locations within the Lower Santa Margarita River Subwatershed Figure 2-9. Reaches and Receiving Water Monitoring Locations within the Upper Santa Margarita River Watershed and Monitored Flow Conditions (Perennial to Dry) 2-31 Figure Priority Water Quality Conditions in the SMR WMA Figure Land Uses within Santa Margarita Watershed Santa Margarita River WMA ii June 2017 Water Quality Improvement Plan [FINAL DRAFT]

4 List of Tables Table 2-1. SMR Subwatersheds and Subareas Table 2-2. Prioritization Step Addressing Assessment of Receiving Water Provisions Table 2-3. Prioritization Step Addressing Assessment of Impacts from MS4 Discharges Provisions Table 2-4. Prioritization Step Identifying Priority Water Quality Conditions Table (d) Listings for the SMR WMA Table 2-6. Trend Analysis of Current versus Historical Water Quality Conditions for Upper SMR Subwatershed Table 2-7. Trend Analysis of Current versus Historical Water Quality Conditions for Lower SMR Subwatershed Table 2-8. Beneficial Uses within the Santa Margarita WMA Table 2-9. Beneficial Use Associated Questions Table Summary of Eutrophication Assessment Results Table Summary of Toxicity Assessment Results Table Assessment Results for Physical Habitat Table Summary of Recreational Beneficial Use Impact Assessment Table Trash Conditions in Upper SMR Subareas Table Dry Weather MS4 Field Screening Trash Assessments for the Lower SMR Subwatershed (Source: TMAR) Table Summary of Municipal Supply Beneficial Use Impact Assessment Table Summary of Food and Industrial Supply Beneficial Use Impact Assessment Table MS4 Contribution to Receiving Water Conditions and Beneficial Use Impacts Identified in Step Table Priority Water Quality Conditions Table Summary of Rationale for Selection of Highest Priority Water Quality Conditions Table Highest Priority Water Quality Conditions Table Santa Margarita WMA Land Use by Copermittee (acres) Santa Margarita River WMA iii June 2017 Water Quality Improvement Plan [FINAL DRAFT]

5 Appendices Appendix 2A Data Summary and Analysis Procedures Appendix 2B Source Evaluation Appendix 2C Potential Strategies to Address the HPWQC Santa Margarita River WMA iv June 2017 Water Quality Improvement Plan [FINAL DRAFT]

6 List of Acronyms BMI Benthic Macroinvertebrate BMP Best Management Practices CEDEN California Environmental Data Exchange Network CRAM California Rapid Assessment Method Index CSCI California Stream Conditions Index CTR California Toxics Rule DWQ Division of Water Quality HPWQC Highest Priority Water Quality Condition IBI Index of Biological Integrity IC/ID Illicit Discharge/Illegal Connection IDDE Illicit Discharge Detection and Elimination JRMP Jurisdictional Runoff Management Programs LID Low Impact Development NPDES National Pollutant Discharge Elimination System OWTS Onsite Wastewater Treatment Systems PWQC Priority Water Quality Condition RCFCWCD Riverside County Flood Control and Water Conservation District RTA Rapid Trash Assessment SMC Stormwater Coalition Monitoring SMR Santa Margarita River SMRNIG Santa Margarita River Nutrient Initiative Stakeholder Group SWAMP Surface Water Ambient Monitoring Program SWRCB State Water Resource Control Board TDS Total Dissolved Solids TMDL Total Maximum Daily Load USEPA United States Environmental Protection Agency USGS United States Geological Survey WMA Watershed Management Area WQI Water Quality Index WQO Water Quality Objective WQIP Water Quality Improvement Plan Santa Margarita River WMA v June 2017 Water Quality Improvement Plan [FINAL DRAFT]

7 2 Priority Water Quality Conditions The Permit requires that the Copermittees identify the water quality conditions associated with MS4 discharges that will be addressed by the Plan. The Permit describes PWQCs as pollutants, stressors and/or receiving water conditions that are highest threat to receiving water quality or that most adversely affect the quality of receiving waters. The goal of the prioritization was to develop a process that utilized available data and information of all types, considered known impacts to beneficial uses, and incorporated local knowledge and information about watercourse function, environmental values, community goals, and habitat preservation among other factors. For evaluation of water quality conditions and as allowed by the Permit, the SMR WMA was separated into two subwatersheds (Upper and Lower SMR subwatersheds) and 13 subareas (6 in the Upper SMR and 7 in the Lower SMR) based on a combination of watershed hydrologic subareas, 2010 Clean Water Act Section 303(d)/305(b) Report, and regional hydrology (see Figure 2-1 and Table 2-1). The prioritization process is described in Section 2.1, with additional details and results of prioritization provided in Sections 2.3 through 2.8. Table 2-1. SMR Subwatersheds and Subareas Upper SMR Subareas Upper Murrieta Creek and Tributaries Warm Springs Murrieta and Long Canyon Creeks Santa Gertrudis Creek Temecula Creek and Redhawk Channel Vail Lake and Pechanga Creek Lower SMR Subareas Upper Santa Margarita River Lower Santa Margarita River Rainbow Creek Sandia Creek De Luz Creek Fallbrook Creek Santa Margarita Estuary Santa Margarita River WMA 2-1 June 2017

8 Figure 2-1. Priority Condition Assessment Subareas Santa Margarita River WMA 2-2 June 2017

9 2.1 PROCESS TO PRIORITIZE WATER QUALITY CONDITIONS The Copermittees developed a prioritization process to identify priority water quality conditions that will be targeted to provide meaningful improvements as well as protect water quality by using the best available information on the condition of the waterbodies in the SMR WMA. The prioritization process was based on information outlined in Provisions B.2.a, B.2.b, and B.2.c of the Permit and considers multiple factors related to beneficial uses and water body conditions to prioritize water quality conditions within the SMR WMA. An overview of the ranking system approach is illustrated by the 5 steps shown in Figure 2-2. Public and Consultation Committee input was also considered as part of the prioritization process (see Appendix 1B). Receiving water conditions in the Upper and Lower SMR Subwatersheds were carefully characterized using an assessment of the information described in Steps 1 through 3 of the prioritization process and outlined in Provision B.2.a of the Permit (See Table 2-2). Following the assessment of the receiving waters, an assessment of the impacts from MS4 discharges was conducted in Step 4 as outlined in Provision B.2.b. of the Permit (see Table 2-3). Step 5A and 5B identified the PWQC and HPWQC as described in Provision B.2.c. of the Permit. The prioritization process was designed to evaluate physical, chemical, and biological factors that could contribute to beneficial use impacts in receiving waters while also complying with the Provisions laid out in the Permit. Steps 1 and 2 are constituent specific analyses designed to identify constituents that may be contributing to PWQCs. Step 3 integrates the constituent analysis with an assessment of other potential conditions that could impact beneficial uses in the watershed along with known information about potential beneficial use impacts. Any condition/subarea combination that does not exceed any of the thresholds used for assessment in Steps 1-3 is not considered a PWQC. All other waterbodies are considered potential PWQCs as determined by the receiving water analysis. This list of potential PWQCs is then assessed for potential impacts from MS4 discharges in Step 4. Any condition/subarea combination where an MS4 discharge has the potential to contribute to a PWQC based on the analysis in Step 5A was identified as a PWQC. These PWQCs are then prioritized to determine the HPWQCs based on 10 considerations related to the beneficial use and receiving water analysis as well as feasibility of potential improvements that can be achieved in Step 5B. All of these steps are described in further detail in Sections below and the data, water quality objectives, and thresholds used for the analyses are described in Appendix 2A. Santa Margarita River WMA 2-3 June 2017

10 Figure 2-2. Prioritization Process for the SMR WMA Santa Margarita River WMA 2-4 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

11 Table 2-2. Prioritization Step Addressing Assessment of Receiving Water Provisions Permit Provision B.2.a. Assessment of Receiving Water Provision 1) Receiving waters listed as impaired on the Clean Water Act Section 303(d) List of Water Quality Limited Segments (303(d) List) 2) TMDLs adopted and under development by the Regional Board 3) Receiving water limitations of Permit Provision A.2 4) Known historical versus current physical, chemical, and biological water quality conditions 5) Sensitive or highly valued receiving waters 1 6) Available, relevant, and appropriately collected and analyzed physical, chemical, and biological receiving water monitoring data 7) Available evidence of erosional impacts in receiving waters due to accelerated flows (i.e., hydromodification) 8) Available evidence of adverse impacts to the chemical, physical, and biological integrity of receiving waters; 9) The potential improvements to the overall condition of the watershed that can be achieved. Prioritization Process Step Addressing Provision Step 1A. Impaired Receiving Waters and Total Maximum Daily Loads Step 1B. Confirmation of Continued Receiving Water Exceedances Step 3. Assessment of Potential Beneficial Use Impacts Step 5B. Determination of Highest Priority Water Quality Conditions Table 2-3. Prioritization Step Addressing Assessment of Impacts from MS4 Discharges Provisions Permit Provision B.2.b. Assessment of Impacts from MS4 Discharges Provision 1) The discharge prohibitions of Provision A.1 and effluent limitations of Provision A.3 2) Available monitoring data from the Copermittees MS4 outfalls 3) Locations of each Copermittees MS4 outfalls that discharge to receiving waters 4) Locations of MS4 outfalls that are known to persistently discharge non-stormwater to receiving waters likely causing or contributing to impacts on receiving water beneficial uses 5) Locations of MS4 outfalls that are known to discharge pollutants in stormwater causing or contributing to impacts on receiving water beneficial uses 6) The potential improvements in the quality of discharges from the MS4s that can be achieved Prioritization Process Step Addressing Provision Step 4. Assessment of Potential MS4 Impacts Step 5B. Determination of Highest Priority Water Quality Conditions 1 Defined in Order No. R as estuaries designated under the National Estuary Program under CWA section 320, marine protected areas, wetlands defined by the State or U.S. Fish and Wildlife Service s National Wetlands Inventory as wetlands, waters having the Preservation of Biological Habitats of Special Significance (BIOL) beneficial use designation, and receiving waters identified as Areas of Biological Significance, or areas recognized as sensitive or highly valued by the Copermittees. Santa Margarita River WMA 2-5 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

12 Table 2-4. Prioritization Step Identifying Priority Water Quality Conditions Permit Provision B.2.c. Identification of Priority Water Quality Conditions 1) The Copermittees must use the information gathered for Provisions B.2.a and B.2.b to develop a list of priority water quality conditions as pollutants, stressors and/or receiving water conditions that are the highest threat to receiving water quality or that most adversely affect the quality of receiving waters. The list must include the following information for each priority water quality condition: (a) The beneficial use(s) associated with the priority water quality condition; (b) The geographic extent of the priority water quality condition within the Watershed Management Area, if known; (c) The temporal extent of the priority water quality condition (e.g., dry weather and/or wet weather); (d) The Copermittees with MS4s discharges that may cause or contribute to the priority water quality condition; and (e) An assessment of the adequacy of and data gaps in the monitoring data to characterize the conditions causing or contributing to the priority water quality condition, including a consideration of spatial and temporal variation. 3) The Copermittees must identify the highest priority water quality conditions to be addressed by the Water Quality Improvement Plan, and provide a rationale for selecting a subset of the water quality conditions identified pursuant to Provision B.2.c.(1) as the highest priorities. Prioritization Process Step Addressing Provision 2) Step 5A. Priority Water Quality Conditions 4) Step 5B. Determination of Highest Priority Water Quality Conditions 2.2 DATA RECEIVED AND ANALYZED Sources of raw data that were available for the receiving water condition assessment, are summarized below. To ensure that all available data were identified, a public call for data was conducted as described in Section Detailed information on the data sources is included in Appendix 2A. One large set of data was provided by the RCFCWCD that included data from the Southern California Stormwater Monitoring Coalition (SMC). Two other datasets were identified during the public call for data. One was the SMRNIG dataset, and one was from the California Environmental Data Exchange Network (CEDEN), which was a combined dataset from US Environmental Protection Agency (USEPA), Southern California Bight, SMC and Surface Water Ambient Monitoring Program (SWAMP). Both datasets are included in the analysis and are compilations that include data from different monitoring programs. CEDEN data are extracted from the CEDEN website and the SMRNIG data are from the water quality database developed for the Hydrological and Biological Support to the Lower Santa Margarita Watershed Monitoring Santa Margarita River WMA 2-6 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

13 Program final report 2. Under these monitoring programs, various types of information and data were collected and assessed including field measurements, field observations, photographs, site/field reconnaissance findings and mapping, chemistry, bioassessment, toxicity, taxa metrics, California Stream Conditions Index (CSCI), Index of Biological Integrity (IBI), Benthic Macroinvertebrates (BMI), hydromodification, and agricultural sources. In addition to these programs, multiple special studies have been performed by the Copermittees. These data provided additional information related to contributions from other sources such as federal, state, and tribal lands, the effects of hydromodification on receiving waters, sediment toxicity, sources of iron and manganese in the watershed, the presence of trash in the watershed, and TMDL related information. All data collected were assessed and considered as part of the analysis process. As part of the assessment, various quality assurance/quality control issues were identified with some datasets, particularly some of the older datasets. These issues included incomplete information on monitoring locations, unclear units, and missing results. As a result, the historic data were used as part of a more qualitative assessment to compare historic conditions to current conditions and the more recent data were used in the quantitative assessment as described in Appendix 2A. 2.3 STEP 1A. IMPAIRED RECEIVING WATERS AND TOTAL MAXIMUM DAILY LOADS (PROVISIONS B.2.A.(1) AND B.2.A.(2)) Step 1A. 303(d) Listings The Clean Water Act Section 303(d)/305(b) Integrated Report identifies impaired receiving waters as required by the federal Clean Water Act and based on the policy set out in the State Water Resources Control Board (SWRCB) s Listing Policy. 3 There are multiple receiving waters in the SMR WMA listed as impaired on the 2010 Integrated Report which are summarized in Table 2-5. The 2010 Integrated Report is currently undergoing an update and a proposed 2014/2016 list of impaired waters is planned to be approved by the SWRCB in Fall While these proposed listings are not included in the 303(d) list assessment because they are not final, the Step 1B assessment includes a review of water quality objective exceedances for constituents in addition to those on the 303(d) list to identify additional constituents that may be contributing to impairments in data collected since the (d) list. 2 Stetson Engineers. Final Report: Hydrological and Biological Support to the Lower Santa Margarita Watershed Monitoring Program Water Years , Prepared by Stetson Engineers Inc., and San Diego State University, February 21, Water Quality Control Policy for Developing California s Clean Water Act Section 303(d) List Appendix A, State Water Resources Control Board, September 30, Santa Margarita River WMA 2-7 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

14 Table (d) Listings for the SMR WMA Water Body Name 4 Upper Santa Margarita Watershed Lower Santa Margarita Watershed Warm Springs Long Canyon Creek 2 Murrieta Creek 2 Santa Gertrudis Creek Temecula Creek 3 Redhawk Channel 3 Santa Margarita River Upper Santa Margarita River Lower Rainbow Creek De Luz Creek Sandia Creek Santa Margarita Estuary Chlorpyrifos Copper Diazinon Escherichia coli (E. coli) Enterococcus Eutrophic Fecal Coliform 1 Iron Manganese Nitrogen Phosphorus Sulfates Total Dissolved Solids Total Nitrogen as N Toxicity 1. Proposed to be delisted on the Regional Water Board approved 2014 Clean Water Act Sections 305(b) and 303(d) Integrated Report for the San Diego Region. State Water Board approval is pending. 2. Both reaches are part of the Murrieta and Long Canyon Creeks subarea. 3. Both reaches are part of the Temecula Creek and Redhawk Channel subarea. 4. There are no 303(d) listings for any waterbodies in the Vail Lake and Pechanga Creek or Fallbrook Creek subareas Step 1A. TMDLs The Rainbow Creek Nutrient TMDL (Water Quality Control Plan for the San Diego Basin (Basin Plan) Amendment: Resolution No. R ) became effective in 2006 to address water quality impairments in Rainbow Creek (San Diego Regional Water Quality Control Board, 2006). The Rainbow Creek TMDL includes targets and allocations to address nitrogen and phosphorus 303(d) listings in Rainbow Creek. In 2013, the Rainbow Creek Nutrient TMDL was incorporated into Attachment E.3 of the MS4 Permit. The County of San Diego is the only Copermittee subject to the Rainbow Creek TMDL. Santa Margarita River WMA 2-8 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

15 In 2011, a broad group of stakeholders (Cities/counties, utility districts, Caltrans, scientists, tribes, NGOs, USGS, Camp Pendleton, Farm Bureau, Regional Water Quality Control Board staff) formed the Santa Margarita River Nutrient Initiative Group (SMRNIG) with the goal of addressing nitrogen and phosphorus 303(d) listings in the Santa Margarita River Watershed. The multi-year process will address the 303(d) listings in four phases: Santa Margarita River Estuary, Lower Santa Margarita River to confluence with De Luz Creek, Upper Santa Margarita River, and the Tributaries to the Santa Margarita River (hereafter called the Upper SMR Subwatershed). The Regional Water Board is currently planning to adopt a TMDL alternative for the Santa Margarita River Estuary in The remaining portions of the watershed will be addressed as funding is available. As part of the development of the TMDL Alternative Resolution for the Estuary, the SMRNIG partner Marine Base Camp Pendleton sponsored SPAWAR to develop an estuary model using monitoring data for total nitrogen, total phosphorus, algal biomass, and dissolved oxygen collected in 2008 and 2009 in the Estuary. The Estuary model predicts the dissolved oxygen and algal biomass concentrations resulting from total nitrogen and total phosphorus loading to the Estuary. Several model scenarios were run to assess the changes in dissolved oxygen and algal biomass concentrations predicted to result from reducing loadings of total nitrogen and total phosphorus to the Estuary. The results of the model scenarios are summarized in the report Application of watershed loading and estuary water quality models to inform nutrient management in the Santa Margarita River Watershed 4 (Model Application Report). In addition to the Estuary model, a watershed loading model was developed by TetraTech on behalf of the Regional Water Board for the Santa Margarita River watershed. The purpose of this model was to predict the loadings from the watershed into the Estuary and estimate the contributions from various land based sources (e.g. agricultural, open space, Caltrans, Federal Lands and MS4s). The watershed loading model was only calibrated at the base of the watershed at the point of entry into the Estuary. As a result, the loading estimates for areas upstream of the Estuary are preliminary and will likely be refined as the future phases are completed. The results of the watershed loading model are also presented in the Model Application Report. While the Rainbow Creek Nutrient TMDL used a numeric interpretation of the narrative Basin Plan objective to derive total nitrogen and total phosphorus targets and associated allocations for various sources, the TMDL alternative for the Estuary is focused on reducing nutrient loading to the Estuary to prevent low dissolved oxygen and benthic community impacts that result from excess algal biomass. As a result, the TMDL alternative will likely have targets based on some combination of dissolved oxygen, algal biomass and benthic community scores rather than total nitrogen and total phosphorus. Then, needed total nitrogen and total phosphorus load reductions to meet those targets in the Estuary (based on the Estuary model scenarios) will be used to develop allocations based on the watershed loading model. To facilitate this process, several technical memoranda have been prepared by stakeholders in the SMRNIG and provided to the Regional Water Board for consideration in their TMDL alternative development. These technical memoranda, combined with the Model Application Report, were used where applicable to inform the analysis for the WQIP. Because the TMDL alternative is still under development, the 4 Sutula, et al., Application of watershed loading and estuary water quality models to inform nutrient management in the Santa Margarita River Watershed. Southern California Coastal Water Research Project Technical Report 933. (Model Application Report) Santa Margarita River WMA 2-9 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

16 information provided in the WQIP is subject to revision once the TMDL alternative is approved. Additionally, as future phases of the project become effective, they will be incorporated into the WQIP as part of the adaptive management process Step 1B. Evaluation of Continued Exceedances and Trends After the list of impaired waters was identified, Step 1B of the prioritization process was conducted to evaluate exceedances of receiving water limitations in current receiving water data ( ) and compare the data to the 303(d) listings, TMDLs, and known historic conditions. For the evaluation, recent exceedances were defined as a receiving water that has not met an applicable water quality objective (WQO) as defined in the San Diego Basin Plan 5 in at least 2 samples and more than 10% of all samples in the reaches of the subarea. The 10% threshold was used as it is an allowable exceedance frequency for most objectives in the San Diego Basin Plan and it approximates the thresholds used for evaluation in the State Water Board s Listing Policy. Comparison of current data to known historic conditions was evaluated through a trends analysis using data from 1998 to 2005 and a qualitative assessment of historic data. The procedures for conducting the evaluation are described in more detail in Appendix 2A. In some cases, 303(d) listings were identified for which the recent data are no longer exceeding water quality objectives. While there were insufficient data to delist the constituents in most cases, the lack of recent exceedances, combined with the trend analysis was determined to be sufficient evidence that these constituents were likely no longer contributing to a PWQC. Figure 2-3 and Figure 2-4 show the constituents with current exceedances in dry and wet weather respectively. Constituents on the 303(d) list for the subarea are highlighted in red in the figures. Results show that on the whole, dry and wet weather water quality in the watershed are both trending towards improvement. Additionally, the analysis identified some constituents in certain reaches on the 303(d) list that are likely no longer exceeding water quality objectives and could potentially meet delisting criteria (e.g., copper, chlorpyrifos). 5 California Regional Water Quality Control Board San Diego Region. Water Quality Control Plan for the San Diego Basin. September 8, 1994 as amended May 17, Santa Margarita River WMA 2-10 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

17 Figure 2-3. Dry Weather Water Quality Objective and Threshold Exceedances in SMR WMA. (Red text designates constituents that are on the 303(d) list, black text denotes constituents not listed on the 303(d) list with 10% exceedances) Santa Margarita River WMA 2-11 June 2017

18 Figure 2-4. Wet Weather Water Quality Objective and Threshold Exceedances in SMR WMA. (Red text designates constituents that are on the 303(d) list, black text denotes constituents not listed on the 303(d) list with 10% exceedances.) Santa Margarita River WMA 2-12 June 2017

19 To provide context for the current conditions of the subarea, historical versus current water quality conditions were assessed using a trends analysis described further in Appendix 2A. For the Upper SMR Subwatershed, the trend analysis used data from and assessed whether the water quality indicator conditions were improving, declining, or stable. For the Lower SMR Subwatershed, previous trends analyses conducted as part of the San Diego County Copermittee annual reports were used and only those constituents with observed trends are summarized. The analyses are presented in Table 2-6 for the Upper SMR Subwatershed and Table 2-7 for the Lower SMR Subwatershed. The analyses were separated into wet and dry weather (shown in red and blue in the tables). Results of the analysis demonstrate that most conditions in the Upper SMR Subwatershed appear to either show no trend or are trending towards improvement. The exceptions include some subareas where conditions are declining for nitrogen, phosphorus, dissolved oxygen, ammonia and fecal coliform. For the Lower SMR Subwatershed, most trends were decreasing with some increasing trends for nitrogen, dissolved selenium, conductivity and surfactants. Santa Margarita River WMA 2-13 June 2017

20 Table 2-6. Trend Analysis of Current versus Historical Water Quality Conditions for Upper SMR Subwatershed Subarea Nitrogen Phosphorus Dissolved Oxygen Pesticides Metals Ammonia Fecal Coliform E. Coli Title 22 Total Dissolved Solids ph Upper Murrieta Creek and Tributaries Warm Springs Murrieta and Long Canyon Creeks Santa Gertrudis Creek Temecula Creek and Redhawk Channel Vail Lake and Pechanga Creek Blanks: no exceedances or insufficient data to calculate trends Trends: red for dry weather; blue for wet weather; = probably improving = improving = probably declining = declining = stable = no trend Santa Margarita River WMA 2-14 June 2017

21 Table 2-7. Trend Analysis of Current versus Historical Water Quality Conditions for Lower SMR Subwatershed Nutrients General Chemistry Metals Physical Chemistry Subarea Nitrogen Phosphorus 1 Ammonia Dissolved Organic Carbon Surfactants (MBAS) Biochemical Oxygen Demand Total Cadmium Dissolved Selenium Dissolved Antimony Conductivity Turbidity Santa Margarita River Upper Santa Margarita River Lower 1 Rainbow Creek Fallbrook Creek De Luz Creek Sandia Creek Santa Margarita Estuary Blanks: no trends reported Trends: red for dry weather; blue for wet weather = probably improving = improving = probably declining = declining = no trend Sources: Transitional Monitoring and Assessment Program Report for the Santa Margarita River Watershed Management Area ( and ). Trends reported for the Lower SMR are for receiving waters. Santa Margarita River WMA 2-15 June 2017

22 2.4 STEP 2. IDENTIFY SIGNIFICANT REGULATORY ACTIONS The second step in the process was to identify constituents that are subject to any significant regulatory action beyond the 303(d) listings and TMDLs. All constituent/subarea combinations that were determined to be subject to a significant regulatory action were identified as potentially contributing to a priority water quality condition. The Statewide Trash Amendments 6 constitute a significant regulatory action affecting all Copermittees with land use jurisdiction over designated priority land uses under the Amendments. According to the Trash Amendments, all areas in the watershed where priority land uses are present are subject to the regulatory action. These include all subareas in the Upper SMR Subwatershed except the Vail Lake and Pechanga Creek subarea, and the Fallbrook Creek subarea in the Lower SMR Subwatershed. No other existing or proposed significant regulatory actions were identified which would require consideration. 2.5 STEP 3. ASSESS POTENTIAL BENEFICIAL USE IMPACTS Once constituents potentially contributing to PWQCs were identified in Steps 1 and 2, additional analysis was conducted to evaluate all other pieces of information gathered per the permit requirements and evaluate the potential impacts on beneficial uses from physical, chemical, and biological factors (Provision B.2.a.(6)). The evaluation consisted of the following: Identifying the beneficial uses designated in the Basin Plan for the SMR WMA and grouping related beneficial uses into assessment categories, associated potential PWQCs, and the physical, chemical, and biological indicators of the potential PWQCs. Assessing locations of known beneficial use impacts in the watershed. Evaluating the biological and physical factors using assessment thresholds as described in Appendix 2A. Incorporating the results from the Steps 1 and 2 analysis for the PWQC indicators by beneficial use category. The results on the assessment described above are summarized in Section by beneficial use category Beneficial Uses in the SMR Subareas The beneficial use evaluation approach accounts for all of the beneficial uses of water within the Upper and Lower SMR Subwatersheds as defined in Chapter 2 of the San Diego Basin Plan. 7 The beneficial uses are grouped together into categories that better describe their protective intent. Then, for each beneficial use category, associated potential PWQCs were identified and the physical, chemical, and biological indicators of the potential PWQC were determined based on the 6 California State Water Resources Control Board Amendment to the Water Quality Control Plan for Ocean Waters of California to Control Trash, and Part I Trash Provisions of the Water Quality Control Plan for Inland Surface Waters, Enclosed Bays, and Estuaries of California 7 California Regional Water Quality Control Board San Diego Region. Water Quality Control Plan for the San Diego Basin. September 8, 1994 as amended May 17, Santa Margarita River WMA 2-16 June 2017

23 available watershed data. The beneficial use category, associated beneficial uses, potential PWQC and associated physical, chemical, and biological indicators are shown in Table 2-8. Table 2-8. Beneficial Uses within the Santa Margarita WMA Beneficial Use Category Associated Beneficial Uses Potential PWQCs Physical, Chemical and Biological Indicators Aquatic Life Use WARM COLD WILD RARE BIOL (limited) SPWN (limited) Eutrophication and Nutrient Loading to TMDL waterbodies Toxicity Physical Habitat Algal biomass Benthic community indices Total Nitrogen Total Phosphorus Dissolved Oxygen Ammonia Pesticides 1 Metals 2 Sediment Physical habitat scores (CRAM) Evidence of erosion and hydromodification Recreation Water Supply Food Supply Industry REC-1 REC-2 MUN GWR AGR IND PROC Nuisance Indicator Bacteria Concentrations Constituents of potential concern for drinking water supplies Constituents of potential concern for agricultural supply Constituents of potential concern for industrial supply Trash Fecal Coliform Enterococcus E. coli Nitrate Title 22 Constituents 3 Total Dissolved Solids Chloride Boron ph Total Dissolved Solids 1. Pesticides include: Organophosphorus, Organochlorine, and Pyrethroid pesticides 2. Metals include: Copper, Nickel, Zinc, and Selenium 3. A full list of Title 22 Constituents is included in Appendix 2A. Relevant constituents based on the analysis include: iron, manganese, color, sulfate and TDS. Santa Margarita River WMA 2-17 June 2017

24 2.5.2 Location of Known Beneficial Uses and Sensitive Receiving Waters For each subarea, a series of questions were used to evaluate areas of the SMR WMA where beneficial uses would be more likely to be impacted as a result of the physical, chemical and biological indicators identified in Table 2-8. Aquatic Life: Sensitive Areas Potentially Impacted? Recreation: Location of Known Recreation and Flow Conditions Supportive of Recreation? Municipal Supply: Location of Known Municipal Supply Diversion? Food Supply: Location of Known Agricultural Supply Diversion? Industrial Supply: Location of Known Industrial Diversion? These questions were meant to help target and identify areas where there were known and active beneficial uses present to prioritize areas that are more likely to be impacted by receiving water conditions. Table 2-9 provides a summary of this analysis. Receiving waters recognized as sensitive or highly valued by the Copermittees are required to be assessed in Provision B.2.a.(3) of the Permit and were used to prioritize locations of potential impacts to the aquatic life beneficial uses. Sensitive receiving waters in the Upper SMR Subwatershed include streams with the Preservation of Biological Habitats of Special Significance (BIOL) designated beneficial use and bodies of water recognized as wetlands by the State or U.S. Fish and Wildlife Service s National Wetland Inventory (NWI). The Lower SMR Subwatershed does not include any BIOL designated waterbodies but does include NWI recognized waterbodies. Sensitive water bodies in the Upper and Lower SMR Subwatersheds are illustrated in Figure 2-5. Procedures for evaluating the location of known recreation and flow conditions supportive of recreation are described in more detail in Appendix 2A. Known locations of recreation beneficial uses were identified in the Murrieta Creek and Long Canyon subarea and all subareas of the Lower SMR Subwatershed. Flow conditions to support recreation were identified in the Warm Springs, Murrieta Creek and Long Canyon, Santa Gertrudis Creek subareas and all subareas of the Lower SMR Subwatershed. Known municipal diversions were identified in the Lower Santa Margarita River subarea. Known agricultural diversions were identified in Sandia Creek and the De Luz Creek subareas. No known industrial diversions were identified in any subarea. Santa Margarita River WMA 2-18 June 2017

25 Table 2-9. Beneficial Use Associated Questions Subwatershed Upper SMR Lower SMR Subarea Upper Murrieta Creek and Tributaries Aquatic Life: Sensitive Areas Potentially Impacted? REC: Location of Known Recreation? REC: Flow Conditions Supportive of Recreation? MUN: Location of Known Municipal Supply Diversion? AGR: Location of Known Agricultural Supply Diversion? IND: Location of Known Industrial Diversion? No No No No No No Warm Springs No No Yes No No No Murrieta and Long Canyon Creek Yes Yes Yes No No No Santa Gertrudis Creek Yes No Yes No No No Temecula Creek and Redhawk Channel Yes No No No No No Vail Lake and Pechanga Creek No No No No No No Upper Santa Margarita River No Yes Yes No No No Lower Santa Margarita River Yes Yes Yes Yes No No Rainbow Creek No Yes Yes No No No Fallbrook Creek No Yes Yes No No No De Luz Creek No Yes Yes No Yes No Sandia Creek No Yes Yes No Yes No Santa Margarita Estuary No Yes Yes No No No Santa Margarita River WMA 2-19 June 2017

26 Figure 2-5. SMR Sensitive Waters Wetlands Defined by the NWI and Cole Creek with BIOL Beneficial Use Santa Margarita River WMA 2-20 June 2017

27 2.5.3 Results of Assessment of Potential Beneficial Use Impacts The potential beneficial use impacts assessment integrates the Step 1 and Step 2 water chemistry assessments with the locations of known beneficial use locations and an evaluation of physical and biological factors to identify potential PWQCs. This section summarizes the results of the analysis of the indicators shown in Table 2-8 for each beneficial use category Aquatic Life Beneficial Use Category Potential impacts to aquatic life were evaluated through assessments of eutrophication, chronic toxicity, and physical habitat Eutrophication The eutrophication potential of streams and impacts to aquatic life were assessed using water chemistry data for nitrogen and phosphorus, as well as available biological condition information for algal biomass and macrobenthic invertebrates. The results of the assessment are summarized in Table Results of the analysis show that many subareas are above the assessment threshold for nitrogen and phosphorus and have the potential to contribute nutrient loading to TMDL waterbodies. Additionally, a few subareas have elevated algal biomass levels, indicating the potential for localized eutrophication concerns. Table Summary of Eutrophication Assessment Results Subwatershed Upper SMR Subarea 303(d) Listings for Associated Chemical Indicators TMDL Nitrogen Above Assessment Threshold Phosphorus Above Assessment Threshold Algal Biomass Above Threshold Upper Murrieta Creek and Tributaries No Yes (1) No D No No Warm Springs Yes Yes (1) D, W D, W D D Murrieta and Long Canyon Creek 3 Yes Yes (1) D, W D, W No D Santa Gertrudis Creek Yes Yes (1) D, W D, W No No Temecula Creek and Redhawk Channel Yes Yes (1) D, W D, W D D Benthic Below Threshold Vail Lake and Pechanga Creek No Yes (1) No No No N/A Upper Santa Margarita River Yes Yes (1) No W No No Lower Santa Margarita River Yes Yes (1) D W No No Rainbow Creek Yes Yes (2) D, W D, W N/A No Lower SMR Fallbrook Creek No No D D, W N/A N/A De Luz Creek Yes Yes (1) No D, W No N/A Sandia Creek No Yes (1) D D, W No No Santa Margarita Estuary Yes Yes (1) D, W D, W N/A N/A N/A: no data for assessment; Threshold exceedance: D for dry weather; W for wet weather 1. TMDL alternative for the SMR Estuary under development that identifies dry weather nutrient loading from the subarea to be potentially contributing to eutrophication concerns in the Estuary. 2. Effective TMDL with dry and wet weather allocations for MS4s. Santa Margarita River WMA 2-21 June 2017

28 Toxicity The assessment of chemical, physical and biological indicators associated with toxicity are summarized in Table The assessment included evaluation of toxicity samples in the SMR WMA and results from exceedance analyses of pesticides, metals, and ammonia conducted in Step 1B. Results of the analysis show that observed toxicity is limited to a few subareas. Constituents potentially contributing to toxicity, including diazinon and copper exceeded thresholds in a few subareas. Additionally, although 303(d) listings for constituents potentially contributing to toxicity exist in most subwatersheds, most of these listings were not confirmed in the Step 1B exceedance analysis and the pesticide trends indicate improving conditions. Table Summary of Toxicity Assessment Results Subwatershed Upper SMR Lower SMR Subarea 303(d) Listings TMDL Toxicity Above Assessment Threshold Pesticides Above Assessment Threshold Metals Above Assessment Threshold Upper Murrieta Creek and Tributaries No No No No No No Warm Springs Yes 6 No N/A No D 3, W 2 No Murrieta and Long Canyon Creek Yes 5 No W W 1 W 2 No Santa Gertrudis Creek Yes 5 No N/A No D 3 No Ammonia Above Assessment Threshold 4 Temecula Creek and Redhawk Channel Yes No D, W D 1 D 2 D, W Vail Lake and Pechanga Creek No No N/A No No No Upper Santa Margarita River Yes No No No No No Lower Santa Margarita River No No No N/A No D, W Rainbow Creek No No N/A N/A No D, W Fallbrook Creek No No No N/A No D De Luz Creek No No N/A N/A No D, W Sandia Creek No No No N/A D D, W Santa Margarita Estuary No No N/A N/A No D, W N/A: no data for assessment; Threshold exceedance: D for dry weather; W for wet weather 1. Diazinon is the only pesticide with exceedances in this subarea 2. Copper is the only metal with exceedances in this subarea. 3. Selenium is the only metal with exceedances in this subarea. 4. The ammonia objective in the Basin Plan is based on older EPA recommended criteria that has been updated. Based on the newer EPA criteria, some of these exceedances may be removed. 5. Listings for chlorpyrifos and copper that were not confirmed during the Step 1B exceedance analysis. 6. Listing for chlorpyrifos that was not confirmed during the Step 1B exceedance analysis. Santa Margarita River WMA 2-22 June 2017

29 Physical Habitat Erosional Impacts (Provision B.2.a.(7)) The assessment of chemical, physical and biological indicators associated with physical habitat are summarized in Table The physical habitat assessment utilizes the California Rapid Assessment Method (CRAM) index which provides an overall summary score for the physical habitat of a monitoring location. The CRAM index and CRAM monitoring results are discussed in more detail in Appendix 2A. In addition, stream conditions and potential areas of erosion and observed hydromodification were considered in the assessment. The Consultation Committee provided comments with areas recommended for investigation for potential erosion/hydromodification concerns in the Upper SMR Subwatershed. These areas, along with the characteristics of the channels are shown in Figure 2-6. Similar information is not available for the Lower SMR Subwatershed and no areas for investigation were identified in the Lower SMR Subwatershed. The results of the assessment showed that the CRAM scores were generally good throughout the SMR WMA, though there were a few areas in the Upper SMR Subwatershed where there is evidence of erosion/hydromodification. Figure 2-6. Upper SMR Subwatershed Channel Characteristics and Areas Identified by Consultation Committee for Investigation Santa Margarita River WMA 2-23 June 2017

30 Table Assessment Results for Physical Habitat Subwatershed Subarea 303(d) Listing TMDL CRAM Score below threshold Evidence of Hydromodification 1 Upper Murrieta Creek and Tributaries No No No 2 (4) Warm Springs No No No 2 Yes Upper SMR Murrieta and Long Canyon Creek 3 No No No 2 Yes Santa Gertrudis Creek No No No No Temecula Creek and Redhawk Channel No No No 2 (4) Vail Lake and Pechanga Creek No No N/A No Upper Santa Margarita River No No No N/A Lower Santa Margarita River No No No N/A Rainbow Creek No No No 2 N/A Lower SMR Fallbrook Creek No No N/A N/A De Luz Creek No No N/A N/A Sandia Creek No No No N/A Santa Margarita Estuary No No N/A N/A N/A: no data for assessment 1. As reported in the Hydromodification Monitoring Project Report 2. As described in Appendix 2A, the CRAM threshold is <50. However, for scores between 50 and 75, physical habitat impacts were considered a PWQC if there was also evidence of hydromodification. These reaches had CRAM scores between 50 and CRAM scores from Murrieta Creek and evidence of hydromodification on Long Canyon Creek 4. Areas are under investigation at the sites identified by the Consultation Committee Recreation The assessment for recreation utilizes indicator bacteria results from the Step 1 analysis and is summarized in Table No other physical or biological indicators were identified as indicators for the recreation beneficial use category. Santa Margarita River WMA 2-24 June 2017

31 Table Summary of Recreational Beneficial Use Impact Assessment Subwatershed Upper SMR Lower SMR Subarea Santa Margarita River WMA 2-25 June (d) Listings TMDL Fecal Coliform Above Threshold E. coli Above Threshold Location of Known Recreation Flow Condition Supportive of Recreation Upper Murrieta Creek and Tributaries No No D D,W No No Warm Springs Yes No D,W D,W No Yes Murrieta and Long Canyon Creek Yes No D,W D,W Yes Yes Santa Gertrudis Creek Yes No D,W D,W No Yes Temecula Creek and Redhawk Channel Yes No D,W D,W No No Vail Lake and Pechanga Creek No No No No No No Upper Santa Margarita River No No No No Yes Yes Lower Santa Margarita River Yes No W No Yes Yes Rainbow Creek No No D,W No Yes Yes Fallbrook Creek No No No No Yes Yes De Luz Creek No No D,W No Yes Yes Sandia Creek No No D,W No Yes Yes Santa Margarita Estuary No No No No Yes Yes Threshold exceedance: D for dry weather; W for wet weather; Nuisance Conditions The Statewide Trash Amendments identify urbanized areas as priority land uses for trash, which has the potential to impact aquatic life and recreational beneficial uses in receiving waters. While the Upper SMR subwatershed and Fallbrook Creek are subject to a regulatory action for trash, additional data available from special studies were assessed to determine if any additional subareas should be added. Based on the special study results, no additional subareas were identified for consideration of a nuisance condition PWQC. Table Trash Conditions in Upper SMR Subareas Subwatershed Subarea Dry Wet Rating Score Rating Score Upper Murrieta Tributaries Optimal 111 Optimal 119 Warm Springs Suboptimal 85 Suboptimal 88 Upper SMR Murrieta Creek and Long Canyon Creek Suboptimal 86 Suboptimal 90 Santa Gertrudis Creek Optimal 107 Optimal 103 Temecula Creek and Redhawk Channel Suboptimal 80 Suboptimal 81 Vail Lake N/A N/A N/A N/A 1 Results from Trash and Litter Investigation Special Study. Study area does not include Lower SMR Subwatershed. 2 Overall ratings and scores based on the Rapid Trash Assessment (RTA) 3 N/A no data for assessment

32 Table Dry Weather MS4 Field Screening Trash Assessments for the Lower SMR Subwatershed (Source: TMAR) Trash Present Copermittee HSA No Trash Present Low (<50 pieces) Medium (50 to 400 pieces) High (>400 pieces) County of San Diego Total Municipal Supply The assessment of chemical indicators associated with municipal supply are summarized in Table 2-16 based on the analysis conducted in Step 1. No physical or biological indicators were identified for consideration for the municipal supply beneficial use category. Table Summary of Municipal Supply Beneficial Use Impact Assessment Subwatershed Upper SMR Lower SMR Subarea Santa Margarita River WMA 2-26 June (d) Listings TMDL Nitrate Above Threshold Title 22 Above Threshold Location of Known Municipal Supply Diversion Upper Murrieta Creek and Tributaries No No No D 1,2 No Warm Springs Yes 1,2 No No D,W 1,2,3,4,5 No Murrieta and Long Canyon Creek Yes 1,2 No No D,W 1,2,4,5 No Santa Gertrudis Creek Yes 1,2 No No D,W 1,2,4,5 No Temecula Creek and Redhawk Channel Yes 1,2,4 No No D,W 1,2,3,4,5 No Vail Lake and Pechanga Creek No No No No No Upper Santa Margarita River No No No D 1 No Lower Santa Margarita River No No D,W D,W 1,2,3,4,5 Yes Rainbow Creek Yes 1,3,4 No D,W D,W 2,3,4 No Fallbrook Creek No No No D,W 1,2,3,4 No De Luz Creek Yes 1,2,3 No No D,W 1,3,4 No Sandia Creek Yes 1,3,4 No No D,W 1,3,4 No Santa Margarita Estuary (6) (6) (6) (6) (6) N/A: no data for assessment; Threshold exceedance: D for dry weather; W for wet weather 1. Iron 2. Manganese 3. Sulfate 4. TDS 5. Color 6. Municipal drinking water beneficial use does not apply to the Santa Margarita Estuary so the analysis was not conducted for this subarea.

33 Food and Industrial Supply The assessment of chemical indicators associated with food and industrial supply are summarized in Table 2-17 based on the analysis conducted in Step 1. No physical or biological indicators were identified for consideration for these beneficial use categories. Table Summary of Food and Industrial Supply Beneficial Use Impact Assessment Subwatershed Subarea Upper Murrieta Creek and Tributaries 303(d) Listings TMDL TDS Above Threshold Chloride Above Threshold Boron Above Threshold ph Above Threshold AGR: Location of Known Agricultural Supply Diversion? IND: Location of Known Industrial Diversion? No No No N/A N/A No No No Warm Springs No No D No N/A No No No Upper SMR Lower SMR Murrieta and Long Canyon Creek Yes No D No No W No No Santa Gertrudis Creek No No D,W D N/A W No No Temecula Creek and Redhawk Channel Vail Lake and Pechanga Creek Yes No D,W No No D,W No No No No No No N/A D No No Upper Santa Margarita River No No No No No No No No Lower Santa Margarita River No No D,W No No No No No Rainbow Creek Yes No D,W No No No No No Fallbrook Creek No No D No No W No No De Luz Creek No No D,W No No W Yes No Sandia Creek Yes No D,W No No W Yes No Santa Margarita Estuary No No No No No No No No N/A: no data for assessment; Threshold exceedance: D for dry weather; W for wet weather; Santa Margarita River WMA 2-27 June 2017

34 2.6 STEP 4. ASSESSMENT OF POTENTIAL MS4 IMPACTS (PROVISION B.2.B) Locations of each Copermittee s MS4 outfalls that discharge to receiving waters (Provision 2.b.(3)) were used to define the geographic areas where MS4 discharges could potentially contribute to receiving water conditions identified in Step 3. Areas without potential MS4 contributions were determined to not be a PWQC. Figure 2-7. Reaches, Major Outfalls with Tributary Areas, and Outfall Monitoring Locations within the Upper Santa Margarita River Subwatershed Santa Margarita River WMA 2-28 June 2017

35 Figure 2-8. Outfall Monitoring Locations within the Lower Santa Margarita River Subwatershed Two subareas, Vail Lake and Pechanga Creek and Sandia Creek, do not receive any MS4 contributions and therefore have no PWQC. For the rest of the subareas, MS4 contributions are a possibility where there are MS4 outfalls and jurisdictional area within or upstream of the subarea. However, in several cases large portions of the subareas do not have the potential for MS4 contributions. As a result, even though a subarea may be identified with a PWQC, the geographic extent is limited to those areas where MS4 discharges may contribute to an identified receiving water PWQC Assessment of MS4 Discharges Available, relevant, and appropriately collected and analyzed storm water and non-storm water monitoring data from Copermittee MS4s (Provision 2.b.(2)) were compared to the discharge prohibitions and effluent limitations (Provision 2.b.(1)) to assess locations of MS4 outfalls that are known to discharge pollutants (Provision 2.b.(5)). MS4 data were then compared to the receiving water assessment to determine if there is potential for the MS4 to be causing or contributing to the receiving water conditions identified in Step 3. Information on locations of MS4 outfalls known to persistently discharge non-storm water to receiving waters was also assessed to help evaluate potential contributions from the MS4. Waterbodies in the Upper SMR Subwatershed are generally non-perennial during dry weather, which results in limited connectivity between MS4 outfalls and Santa Margarita River WMA 2-29 June 2017

36 receiving waters during dry weather. Field data indicate that often, flows from outfalls in the Upper SMR Subwatershed do not reach receiving waters in dry weather conditions, with ponded conditions or a complete lack of flow noted frequently. Additionally, in many cases, site visits indicated that receiving waters, especially in the Upper SMR Subwatershed were dry. Receiving water and outfall sites that were observed to be dry during site visits are indicated by a designation of visited not sampled or VNS. The percentage of time that a site was dry during site visits is shown in Figure 2-9. There are only eight outfall locations within the Upper SMR Subwatershed where water quality data have been collected, although the data record typically spans several years. While this data generally characterizes the discharges from the MS4s, the limited spatial extent of the MS4 outfall data in combination with the non-perennial nature of the waterbodies present challenges for determining the geographic extent of where MS4 discharges actually reach and potentially impact the receiving waterbodies. Thus, the assessment of the potential impacts from MS4 outfalls for a whole subarea based on limited outfall data and waterbodies that may have limited connectivity to the MS4 is challenging, and the results may not be fully representative of conditions across the whole subarea (discussed further in Section 2.7.2). However, in wet weather, all outfalls in the Upper SMR Subwatershed appeared to discharge to receiving waters. The Lower SMR Subwatershed is similar to the Upper SMR Subwatershed in that there is connectivity from the MS4 to receiving water during wet weather, but that is not always the case during dry weather. Although these data limitations exist, the available MS4 data were considered representative for the purposes of the analysis. At least one MS4 monitoring location was available in every subarea with MS4 discharges with the exception of Vail Lake and Pechanga Creek, Sandia Creek, and Santa Margarita Estuary subareas. If the MS4 data contained exceedances of constituents that were also observed in receiving waters within the subarea under the same condition (dry or wet), the MS4 was considered to be potentially contributing and the condition was identified as a PWQC. If exceedances were not observed, the MS4 was not considered to be contributing and the condition was not identified as a PWQC. Further investigation of the connectivity and contribution of MS4s to the PWQCs will be conducted as part of the Monitoring and Assessment Program and may result in refinement of the PWQCs or the geographic extent of these conditions. The potential for non-storm water discharges to cause or contribute to impacts on beneficial uses was assessed in the same method as storm water discharges. Table 2-18 presents a summary of the MS4 contribution to receiving water conditions identified in Step 3. Impacts are summarized by wet and dry season and organized according to beneficial use category. Santa Margarita River WMA 2-30 June 2017

37 Figure 2-9. Reaches and Receiving Water Monitoring Locations within the Upper Santa Margarita River Watershed and Monitored Flow Conditions (Perennial to Dry) VNS = Visited Not Sampled (dry or discontinuous channel or outfall) Santa Margarita River WMA 2-31 June 2017

38 Table MS4 Contribution to Receiving Water Conditions and Beneficial Use Impacts Identified in Step 3 Watershed Upper SMR Lower SMR Subarea Aquatic Life Eutrophication Nitrogen Phosphorus Beneficial Use Category / Water Quality Indicators Toxicity Recreation Water Supply Food and Industrial Supply MS4 contribution to threshold exceedance: D for dry weather; W for wet weather; N/A: no data for assessment 1. Diazinon is the only pesticide observed as having exceedances in receiving waters. No outfall data for diazinon are available. Other pesticides, particularly bifenthrin that may contribute to toxicity have been observed above thresholds in these outfalls, but receiving water data for other pesticides did not exceed thresholds. 2. A special study was conducted in the Upper SMR Subwatershed that indicates the primary source of iron and manganese in the receiving waters and outfall data is natural (see discussion in Appendix 2A). 3. No MS4 outfalls are present in this subarea. For the Santa Margarita Estuary, no MS4 monitoring locations are present in the subarea, but upstream MS4 discharges contribute to the Estuary and have the potential to contribute to any PWQC identified in the receiving waters in the Estuary. Pesticides Upper Murrieta Creek and Tributaries No D,W No No No D,W D,W No W No No Warm Springs D,W D,W No No No D,W D,W No D,W No D Murrieta and Long Canyon Creek D,W D,W (1) W No D,W D,W No D,W No D,W Santa Gertrudis Creek D,W D,W No No No D,W D,W No D,W N/A D,W Temecula Creek and Redhawk Channel D,W D,W (1) No No D,W D,W No D,W No D Vail Lake and Pechanga Creek 3 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A Upper Santa Margarita River No No No No No No No No No No No Lower Santa Margarita River D No N/A No D,W No No No D No D Rainbow Creek D,W D,W N/A No D,W No No D,W D,W No D,W Fallbrook Creek D W N/A No D,W No No No D No D De Luz Creek No No N/A No D,W D No No D No No Sandia Creek 3 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A Santa Margarita Estuary 3 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A Metals Ammonia Fecal Coliform E. Coli Nitrate Title 22 2 ph TDS Santa Margarita River WMA 2-32 June 2017

39 2.7 PRIORITY WATER QUALITY CONDITIONS Priority Water Quality Conditions (Provisions B.2.c.(1)(a-d)) PWQCs are defined by the Permit as pollutants, stressors and/or receiving water conditions that are a highest threat to receiving water quality or that most adversely affect the quality of receiving waters. PWQCs were determined based on the analysis conducted in Steps 1-4. The summary tables in Section combined with the assessment of MS4 contributions in Table 2-18 and input from the public and Consultation Committee were used to determine the PWQCs. If the potential PWQC had a confirmed 303(d) listing, other associated water quality indicator exceedances, other physical or biological threshold exceedances, or a TMDL and MS4s could potentially be contributing to the PWQC in the subarea, the subarea was assigned the PWQC. If these conditions were not met, then the subarea was not assigned to the PWQC. Table 2-19 summarizes the results of this analysis and present the beneficial use category, geographic and temporal extent, and the responsible Copermittees for each PWQC. The industrial supply BU category did not have any identified PWQCs because no industrial diversions were identified and the related exceedances of TDS are addressed by the agricultural BU category PWQCs. Table Priority Water Quality Conditions BU Category Priority Water Quality Condition Temporal Extent Geographic Extent Responsible MS4 Discharge Copermittee(s) Eutrophication (elevated algal biomass) Dry SMR Estuary 3, Warm Springs, Redhawk Channel All Copermittees Aquatic Life Use: Eutrophication Aquatic Life Use: Toxicity Aquatic Life Use: Physical Habitat Nutrient loading to TMDL waterbody Observed toxicity 1 Lowered physical habitat scores (CRAM) or evidence of hydromodification / erosional impacts Dry Rainbow Creek, Subareas with dry weather MS4 discharges that could All Copermittees potentially reach the SMR Estuary 3 Wet Rainbow Creek San Diego County Dry Wet Wet Temecula Creek and Redhawk Channel Murrieta Creek and Long Canyon Warm Springs, Murrieta Creek and Long Canyon RCFCWCD Riverside County Temecula Menifee Murrieta Temecula RCFCWCD Riverside County Wildomar Menifee Murrieta RCFCWCD Riverside County Temecula Wildomar Santa Margarita River WMA 2-33 June 2017

40 BU Category Aquatic Life Use / Recreation: Nuisance Conditions Recreation Water Supply Agricultural Supply Priority Water Quality Condition Trash Indicator Bacteria Concentrations Constituents of potential concern for drinking water supplies (Iron, Manganese) Constituents of potential concern for agricultural supply (TDS) Temporal Extent Dry Wet Dry Wet Dry Wet Dry Wet Geographic Extent All Upper SMR subareas except Vail Lake in areas of priority land uses 2, Fallbrook Creek All Upper SMR subareas except Vail Lake in areas of priority land uses 2, Fallbrook Creek Warm Springs, Murrieta Creek and Long Canyon, Santa Gertrudis Creek, De Luz Creek Warm Springs, Murrieta Creek and Long Canyon, Santa Gertrudis Creek All Upper SMR subareas except Vail Lake, All Lower SMR subareas except SMR Estuary and Sandia Creek All Upper SMR subareas except Vail Lake and Upper Murrieta Creek and tributaries, Rainbow Creek Warm Springs, Santa Gertrudis Creek, Murrieta Creek and Long Canyon, Temecula Creek and Redhawk Channel, Lower SMR, Rainbow Creek, Fallbrook Creek Santa Gertrudis Creek, Murrieta Creek and Long Canyon, Rainbow Creek Responsible MS4 Discharge Copermittee(s) All Copermittees All Copermittees All Copermittees Menifee Murrieta Temecula RCFCWCD Riverside County Wildomar All Copermittees All Copermittees All Copermittees All Copermittees 1. Exceedances of copper, selenium and ammonia were observed in some other reaches, but no toxicity data are available to confirm potential impacts of these exceedances. As discussed previously, the ammonia exceedances may be the artifact of using old criteria and are likely not representative of potential impacts to beneficial uses. The copper exceedances occurred in Warm Springs and the selenium exceedances occurred in Santa Gertrudis Creek, but there is no evidence these exceedances contributed to beneficial use impacts. 2. Priority land uses are defined in the Statewide Trash Amendments. 3. MS4 discharges within the following subareas may reach the Estuary during dry weather and contribute to the Eutrophication PWQC in the Santa Margarita Estuary: Upper Murrieta Creek and Tributaries, Warm Springs, Santa Gertrudis, Murrieta Creek and Long Canyon, Temecula Creek and Redhawk Channel, Upper Santa Margarita River, Lower Santa Margarita River, Rainbow Creek and De Luz Creek. Santa Margarita River WMA 2-34 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

41 Figure Priority Water Quality Conditions in the SMR WMA Santa Margarita River WMA 2-35 June 2017

42 2.7.2 Monitoring Data Adequacy and Data Gaps (Provision B.2.c.(1)(e)) Data gaps were evaluated for the SMR WMA analyses of receiving water conditions and potential impacts from MS4 discharges. Receiving water conditions were found to have data gaps for specific analyses, particularly for biological indices, toxicity, algal biomass and physical habitat. Other data sets for receiving water assessments (e.g., chemistry) were adequate to assess receiving waters conditions. Data to characterize MS4 discharges is spatially limited, particularly in the Upper SMR Subwatershed. Thus, MS4 outfall data is a limiting factor in gaining a comprehensive picture of the MS4 contribution to watershed conditions. Moving forward in the development of goals, strategies, and the monitoring program, data gaps will be further evaluated by identifying specific questions to support assessment of watershed condition and implementation to address PWQCs. Work that will support filling some data gaps may be conducted as part of the SMRNIG pursuant to the availability of grant funds. 2.8 STEP 5B. HIGHEST PRIORITY WATER QUALITY CONDITION (PROVISION B.2.C.(2)) The HPWQCs to be addressed by the WQIP were selected from the list of PWQCs by evaluating them against a set of ten considerations outlined in Table These first seven considerations include many of the components evaluated in Prioritization Steps 1-4 including existence of a TMDL/significant regulatory action, impaired waters 303(d) listing, current WQO and threshold exceedances, as well as historic conditions, location, and geographic extent of the conditions. The last three questions used in the assessment consider potential improvements in condition of waterbodies in the WMA and MS4 discharge quality that can be achieved as stated in Provisions B.2.a.(9) and B.2.b.(6) in the Permit. Each of the PWQCs was given a binary score of 1 if it met the consideration or 0 if it did not. These scores were then summed to give a final score to each of the PWQCs out of a highest possible score of 10. These total scores were then used to rank the PWQCs such that the highest score determined the HPWQC. Based on the assessment of HPWQC considerations, eutrophication in the aquatic life beneficial use category was determined to by the HPWQC (See Table 2-21) over recreation, water supply and food supply beneficial use categories. In general, the scoring reflects the limited geographic scope of other PWQCs and the lack of evidence of beneficial use impacts, combined with limited availability of technology available to effectively treat all constituents affecting recreation, water supply, and food supply. Given the 303(d) listings, existing TMDL, and TMDL alternatives under development for nutrients and biostimulatory substances that cover most subareas in the WMA, the potential impact on aquatic life from those conditions, and the threshold exceedances observed throughout the WMA, eutrophication has been identified as the clear HPWQC. The eutrophication HPWQC includes subareas with observed eutrophication impacts (elevated algal biomass and impacted benthic scores) and dry weather nutrient loading to those subareas to address the eutrophication, and dry and wet weather nutrient loading to Rainbow Creek to address the Rainbow Creek TMDL. The intent of the WQIP is to address the HPWQCs identified through this prioritization process. As implementation progresses and more information is collected to support the prioritization process, Copermittees could determine that other watershed conditions are of a higher priority or that addressing an identified priority may not result in the most beneficial or cost-effective way to Santa Margarita River WMA 2-36 June 2017

43 protect beneficial uses. If this were to occur, the Copermittees may choose to change their focus, and potentially adjust their priorities, as part of the adaptive management process. Santa Margarita River WMA 2-37 June 2017 Water Quality Improvement Plan [FINAL DRAFT]

44 Table Summary of Rationale for Selection of Highest Priority Water Quality Conditions Beneficial Use Category Aquatic Life Aquatic Life/ Rec Considerations TMDL existing/under development (2.a.2) or significant regulatory action (d) Listing (2.a.1) Threshold exceedances (to assess 2a.4-RWL, 2.a.6-analysis of physical, chemical, and biological RW data, 2.a.8 evidence adverse impacts to waterbody integrity): Current WQO exceedances (water chemistry) Current threshold exceedances (other indicators) or evidence of impacts (2.a.7) Known historical compared to current conditions (2.a.5) (increasing trends) 1 Known locations of potential beneficial use impacts Geographic extent (majority of subareas have PWQC +1) Assessment of potential improvements in condition of WMA and MS4 discharge quality that can be achieved (2.a.9 and 2.b.6) based on score from following questions: Feasible projects or programs that could be considered to improve PWQCs? If PWQCs are improved through actions taken by the MS4s, would opportunities related to the beneficial use be realized? Eutrophication Toxicity Physical Habitat Nuisance (Trash) Are there other social benefits gained by restoring the beneficial uses? Total Recreation Water Supply Food Supply Santa Margarita River WMA 2-38 June 2017

45 Table Highest Priority Water Quality Conditions BU Category Eutrophication Priority Water Quality Condition Eutrophication (elevated algal biomass) Nutrient loading to TMDL waterbody Temporal Extent Geographic Extent SMR Estuary Dry 2, Warm Springs, Redhawk Channel 1 Rainbow Creek 1, Subareas with dry weather MS4 discharges that Dry could potentially reach the SMR Estuary 1 Wet Rainbow Creek 1 1. Other areas may be added as result of TMDL alternative development during adaptive management process. 2. MS4 discharges within the following subareas may reach the Estuary during dry weather and contribute to the Eutrophication PWQC in the Santa Margarita Estuary: Upper Murrieta Creek and Tributaries, Warm Springs, Santa Gertrudis, Murrieta Creek and Long Canyon, Temecula Creek and Redhawk Channel, Upper Santa Margarita River, Lower Santa Margarita River, Rainbow Creek and De Luz Creek. 2.9 IDENTIFICATION OF MS4 SOURCES OF POLLUTANTS AND/OR STRESSORS Permit Provision B.2.d requires that the Copermittees identify and prioritize known and suspected sources of stormwater and non-stormwater pollutants and/or stressors associated with discharges that cause or contribute to the highest priority water quality conditions as identified under Provision B.2.c. The identification of known and suspected sources of pollutants and/or stressors that cause or contribute to the HPWQCs considered the following: 1. Pollutant generating facilities, areas, and/or activities with the watershed; 2. Locations of the Copermittee s stormwater conveyance systems; 3. Other known and suspected sources of non-stormwater or pollutants in stormwater discharges to receiving waters within the watershed; 4. Review of available data; and 5. Adequacy of available data to identify and prioritize sources and/or stressors associated with MS4 discharges. The items listed above were used to identify pollutants and stressors that potentially contribute to the HPWQC. A detailed evaluation is provided in Appendix 2B. This Plan considers watershed conditions and priorities in the context of the Copermittees obligations to control MS4 discharges, and the evaluation of potential sources of the HPWQC focuses on MS4 discharges. Where sources are outside of the regulatory authority or controllability of the Copermittees and these sources are impacting water quality within the WMA, the Copermittees may consider opportunities to collaborate with other entities to control the sources of nutrients. Sources described in this section are not exhaustive, but are generally representative of the types of sources present within the WMA. The identification of sources focused on land uses and other sources of pollutants that can contribute total nitrogen and total phosphorus loading to the WMA. Reducing nutrient loading from watershed sources will address both elements of the HPWQC eutrophication (elevated biomass) and nutrient loading to TMDL waterbodies. Santa Margarita River WMA 2-39 June 2017

46 Based on the watershed modeling performed for the SMRNIG to support development of the SMR Estuary TMDL alternative 8, and described in Appendix 2B, several land use categories have been identified as having potential to contribute loads of total nitrogen and total phosphorus to the SMR WMA. The model identifies irrigated agriculture, orchards, vineyards and nurseries, open scrublands and grasslands, and residential land uses as the largest contributors of total nitrogen load to the Santa Margarita River. The model identifies total phosphorus loading as being contributed by roads, orchards, vineyards and nurseries, open scrublands and grasslands, and residential land uses. Many of the land uses that the model identifies as contributing to nutrient loading can be found within the reaches the Copermittees have identified as impacted by eutrophic conditions and/or nutrient loading. Open space, federal and tribal areas, streets, and urban residential areas occupy a high percentage of the MS4 influenced drainage area within the Upper SMR Subwatershed. Within the Lower SMR Subwatershed, agriculture (including orchards and vineyards, as well as field crops and other forms of intensive agriculture) is the second largest land use within the MS4 influenced drainage area, and open space areas and streets are also found within the MS4 influenced drainage area. Within certain subareas (e.g., Redhawk Channel in the Upper SMR Subwatershed), agriculture is present in areas upstream and may serve as a potential source of nutrients if there is connectivity from those upstream areas to the receiving water. However, agriculture is typically located upstream of the MS4 influenced areas in the Upper SMR Subwatershed. The land uses by Copermittee are shown in Table 2-22 and the land uses in the watershed are shown in Figure Sutula, M., J. Butcher, C. Boschen, M. Molina Application of watershed loading and estuary water quality models to inform nutrient management in the Santa Margarita River Watershed. Southern California Coastal Water Research Project (SCCWRP) Technical Report 933. Santa Margarita River WMA 2-40 June 2017

47 Table Santa Margarita WMA Land Use by Copermittee (acres) Land Use a City of Menifee City of Murrieta City of Temecula City of Wildomar County of Riverside Riverside County Flood Control and Water Conservation District Agriculture , ,389 28,053 7% Commercial 31 1,028 1, ,675 1% Industrial ,149 0% Open space 108 3,941 2,939 3,488 42, ,100 56,236 13% Parks and Recreation , ,409 1% Rural Residential 540 7,185 6,832 5, , , ,423 31% Streets 72 6,468 6,499 1,794 8, ,401 6% Urban Residential 32 4,919 5,240 1,554 2, ,540 4% a. Other land uses not within the Copermittees jurisdiction comprise the remaining percentage (37%) of land uses found within the Upper and Lower Santa Margarita River Watershed, totaling 156,185 acres. These land uses are comprised of Federal and Tribal Lands, as well as vacant, undeveloped land, and waterbodies. Residential land uses (35%) comprise the largest proportion of land use within the Upper and Lower SMR WMAs, followed by open space (13%). Commercial and industrial together make up about 1% of the total SMR WMA area. Agriculture (8%) comprise a small percentage of land use in both watersheds. The largest land use category is comprised of land uses not within the Copermittees jurisdiction (37%) including federal and tribal lands, as well as vacant, undeveloped land and waterbodies. Figure 2-11 illustrates the distribution of land uses and activities within the Upper and Lower SMR WMA. County of San Diego Total % of Land Use Santa Margarita River WMA 2-41 June 2017

48 Figure Land Uses within Santa Margarita Watershed Santa Margarita River WMA 2-42 June 2017