Santa Margarita River and Estuary


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. It 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, 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 2018 and alternative to a TMDL was adopted for the Santa Margarita Estuary. Eutrophic conditions cause dissolved oxygen concentrations to fall below 5 mg/l, making it difficult for the Estuary and River to support healthy aquatic life. The eutrophic condition of the Estuary and River is the result of excess nutrient inputs causing overabundant algal growth and the algal life cycle consuming more oxygen than it produces. Nutrients (Total Nitrogen and Total Phosphorus) discharged into the Estuary and River from the surrounding Watershed stimulate excessive algal growth


In 2012 the Santa Margarita River was added to the 303(d) list for nutrients (nitrogen and phosphorus), and the most recent 2014/2016 303(d) list includes nutrients as pollutants in the lower 19 miles and upper 18 miles of the Santa Margarita River. The TMDLs are currently in development.


The alternative to a TMDL for the Santa Margarita Estuary addresses eutrophication through the adoption of load and waste load allocations into municipal separate stormwater (MS4) permits, national pollutant discharge elimination system (NPDES) permits, agricultural waste discharge requirements (WDRs), and working with the primary dischargers to reduce nutrient loads. Two sources of nutrients to the Estuary, treated sewage and groundwater dewatering from a transit project, have been eliminated. Remaining upland nutrient sources are mainly urban and agricultural runoff.

The San Diego Water Board in collaboration with the Santa Margarita River Estuary Watershed Nutrient Initiative Stakeholder Group developed a project to calculate proposed TMDLs for the Estuary, identify the numeric targets, and the reduction in pollutant loadings necessary to restore beneficial uses of the Estuary. These calculations are presented in The Santa Margarita River Estuary, California Nutrients Total Maximum Daily Load Project Staff Report in Appendix A. An Investigative Order was issued in May 2019 to assess the condition of the Estuary and to evaluate the linkage between the nutrient loading trends resulting from implementation actions by the dischargers, and the restoration of the water quality and beneficial uses in the Estuary. Monitoring begins in April 2020 and continues through October 2023.


303(d) Listings

Public Documents


303(d) Listings

  • Detailed 303(d) Listing Information for the Santa Margarita Lagoon/Estuary

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)

Email or call Lark Starkey at or (619) 521-3001 for a copy of documents without links.

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