Santa Margarita River and Estuary

INTRODUCTION

The roughly 750 square mile Santa Margarita River Watershed (Watershed) is located in San Diego and Riverside Counties and drains to the Pacific Ocean just north of the City of Oceanside. The Watershed includes parts of the Cleveland National Forest, the Santa Rosa Plateau Ecological Preserve, and Agua Tibia Wilderness. It also includes portions of the Pechanga, and Cahuilla Indian Reservations, the cities of Murrieta and Temecula, the community of Fallbrook, and portions of the Marine Corps Base Camp Pendleton. The principal land uses in the Santa Margarita Watershed are open space, developed land, agricultural land, and military facilities that include open space. Open space in the Santa Margarita Watershed plays a vital role as a wildlife corridor between the Santa Ana Mountains and Inland San Diego and provides habitat to hundreds of native species and critical habitat for threatened and endangered species including the Southern California steelhead (Oncorhynchus mykiss).

The Santa Margarita River originates at the confluence of Murrieta Creek and Temecula Creek near the City of Temecula at the southern end of the Santa Ana Mountains, with the lower reach originating at the confluence of De Luz Creek and the Santa Margarita River. The 19 miles of the lower Santa Margarita River flows through the Marine Corps Base Camp Pendleton and discharges to the Pacific Ocean through the Santa Margarita Estuary.

The San Diego Water Board first identified nutrient impairments in the Santa Margarita Watershed in the 1980's and in 1986 the Santa Margarita Estuary was added to the Clean Water Act (CWA) section 303(d) List of Water Quality Limited Segments (303(d) list) for eutrophic conditions. In 2005 a Total Maximum Daily Load (TMDL) for nitrogen and phosphorus was adopted for Rainbow Creek and in 2019 an Investigative Order was adopted for the Santa Margarita Estuary.

The eutrophic conditions of the Estuary and River are the result of excess nutrient inputs (total nitrogen and total phosphorus) causing overabundant algal growth which consumes more oxygen than it produces. This causes dissolved oxygen concentrations to fall below 5 mg/l, impeding the Estuary and River's ability to support the Southern California steelhead and healthy aquatic life.

SANTA MARGARITA RIVER NUTRIENT ADVANCE RESTORATION PLAN

The Santa Margarita River (River) was added to the Clean Water Act (CWA) section 303(d) list of Impaired Waters for nutrients (nitrogen and phosphorus) in 2012. Excessive nutrient loading to the River and its tributaries cause and/or contribute to exceedances of Water Quality Objectives and adversely impacts the Cold Freshwater Habitat (COLD), Warm Freshwater Habitat (WARM), and Rare, Threatened, or Endangered Species (RARE) beneficial uses designated to the River. Excessive discharge of nutrients also has the potential to adversely impact the Municipal and Domestic Supply (MUN) beneficial use through impact to large groundwater basins in the Santa Margarita watershed (Watershed). Furthermore, nutrients discharged to the surface waters and groundwater in the Watershed have been shown to contribute to the eutrophication impairment of the Santa Margarita River Estuary (Estuary). Major sources of nutrients to the River include Municipal Separate Storm Sewer Systems (MS4s) and agricultural land uses in San Diego and Riverside counties.

To address the impairment, the objective of the Santa Margarita River Nutrient Advance Restoration Plan (Advance Restoration Plan or ARP) is to reduce nutrient loads entering the River and achieve numeric targets in order to restore and maintain the chemical, physical, and biological integrity of the River and Estuary.

To achieve this, staff are developing the Advance Restoration Plan to address impairments for nutrients and eutrophication in the River consistent with the Impaired Waters Policy. The Advance Restoration Plan relies on implementing existing permits, policies, and plans and tracking the effectiveness of the permits, policies, and plans in achieving nutrient load reductions, numeric targets, and beneficial uses through monitoring.

This approach is consistent with 2023 memorandum from the United States Environmental Protection Agency outlining Advance Restoration Plans as an option states, territories, and authorized tribes can pursue prior to the development of Total Maximum Daily Loads (TMDLs). The memorandum describes an Advance Restoration Plan as a near-term plan or description of actions, with a schedule and milestones, that can in some cases be more immediately beneficial or practicable than a TMDL in achieving water quality objectives. Advance Restoration Plans are not substitutes for TMDLs, and impaired waters for which a state, territory, or authorized tribe pursues an ARP will remain on the Clean Water Act Section 303(d) List and still require a TMDL until water quality objectives are attained. Should the San Diego Water Board approve the Advance Restoration Plan, the County of San Diego, the County of Riverside, and enrollees to agricultural waste discharge requirements (WDRs) in the Watershed may be required to track the progress towards attainment of water quality objectives, or other numeric targets, as specified in a subsequent investigative order.

The draft Advance Restoration Plan has undergone an external scientific peer review, and San Diego Water Board staff are currently preparing their response to peer review comments. The ARP will undergo a public review and comment period in 2025, during which San Diego Water Board staff will hold a workshop to discuss the ARP and answer questions from the public. The draft ARP will likely include the nutrient assimilative capacity of the river that corresponds with Basin Plan objectives (1.0 mg/L total nitrogen and 0.1 mg/L total phosphorus), and numeric targets for dissolved oxygen, chlorophyll-a, and the Algal Stream Condition Index (ASCI). The ARP incorporates a climate change analysis and input from studies funded by the Santa Margarita River Watershed Nutrient Initiative Group, a stakeholder group that has been working on nutrient issues in the Watershed since 2012. The numeric targets represent values that once attained and sustained, should result in water quality that supports the beneficial uses of the River. The Advance Restoration Plan contains many of the same elements of a TMDL, and the San Diego Water Board could adopt a TMDL and Basin Plan amendment based on the findings from the ARP at a future date. However, if the Advance Restoration Plan results in the attainment of water quality standards and the river’s removal from the CWA 303(d) impaired waters list, a TMDL would no longer be required. Staff will likely prepare an Investigative Order to monitor and assess effectiveness of the ARP’s implementation for consideration by the San Diego Water Board.  

SANTA MARGARITA RIVER PUBLIC DOCUMENTS AND LINKS

303(d) Listings

Public Documents

SANTA MARGARITA RIVER AND ESTUARY NUTRIENT WATER QUALITY RESTORATION PLAN

The Santa Margarita River Estuary (Estuary) is a 192-acre area of valuable estuarine habitat including mudflats, salt pannes, salt marsh, and subtidal habitats. This unique estuarine habitat provides important refuge, foraging areas, and breeding grounds for several threatened and endangered species, as well as coastal marine fisheries species. It is located along the southern California coast in northern San Diego County, on the southwestern edge of the U.S. Marine Corps Base Camp Pendleton at the terminus of the Santa Margarita River Watershed (Watershed).

The Estuary was added to the Clean Water Act (CWA) section 303(d) List of Water Quality Limited Segments for eutrophic conditions in 1986 and the impairment was confirmed in by the Southern California Coastal Water Research Project (SCCWRP) during an impairment assessment conducted between 2008 and 2009, in response to an Investigative Order (No. R9-2006-0076) issued by the San Diego Water Board (McLaughlin et al. 2013). To address the eutrophication impairment, for which the causative pollutants are total nitrogen and total phosphorus, the San Diego Water Board collaborated with the Santa Margarita River Watershed Nutrient Initiative Stakeholder Group to develop the Santa Margarita River Estuary Water Quality Restoration Plan (Estuary Restoration Plan). Primary sources of nutrients to the Estuary are agricultural discharges to surface waters throughout the Watershed, agricultural discharges to groundwater from the former Stuart Mesa agricultural fields, and municipal separate storm sewer systems (MS4s).

The Estuary Restoration Plan includes a calculation of proposed TMDLs for the Estuary, numeric targets, and the reduction in pollutant loadings necessary to restore beneficial uses of the Estuary. To achieve the numeric targets and restore the Estuary, a 76 percent reduction in total nitrogen and total phosphorus is required. The Estuary Restoration Plan is implemented though existing permits, policies, and plans and tracks the effectiveness of the permits, policies, and plans in achieving nutrient load reductions, numeric targets, and beneficial uses through monitoring in accordance with Investigative Order R9-2019-0007.

Monitoring for Investigative Order R9-2019-007 began in April 2020 and continued through October 2024. It is expected that a new comprehensive Investigative Order will be developed to encompass both the Santa Margarita River and the Santa Margarita River Estuary. The new Investigative Order will accompany the Santa Margarita River ARP staff report. The Dischargers and the San Diego Water Board will determine whether any adaptive management and monitoring modifications are needed at that time. If the Estuary is not improving, as measured by attainment of numeric target and nutrient reduction milestones, adaptive management actions will be triggered, and the San Diego Water Board will consider if the Estuary Restoration Plan is on track or should be re-assigned to a higher priority for future TMDL development.

SANTA MARGARITA ESTUARY PUBLIC DOCUMENTS AND LINKS

303 (d) LISTINGS

Public Documents

  • Investigative Order R9-2019-0007 (May 2019)
    • APPENDIX A: Santa Margarita Estuary, California. Nutrients Total Maximum Daily Load Project Staff Report (July 2018).
    • Watershed Model Nutrient Loading Estimates for Water Year 2008 (Butcher et al. 2017b)

Santa Margarita Nutrient Initiative Stakeholder Group Documents (Including Investigative Order Workplan, Quality Assurance Project Plan, and Annual Reports)

Email Riley Nolan at Riley.Nolan@waterboards.ca.gov for a copy of documents without links.

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