Major San Diego County Rivers

Each of the major rivers in San Diego County are part of a much larger drainage system, or watershed, consisting of tributaries and a system of lakes, reservoirs, streams and creeks.  The watersheds create valuable habitat for San Diego's diverse animal and plant life, supply water to both rural and urban areas, and offer many recreational opportunities.


Santa Margarita River

The Santa Margarita River is formed near the City of Temecula in Riverside County at the confluence of the Temecula and Murrieta creek systems.  Once formed, the majority of the Santa Margarita River main stem flows within San Diego County through unincorporated areas, the community of Fallbrook, and the Marine Corps Base Camp Pendleton.  The lower river and estuary have largely escaped the development typical of other regions of coastal Southern California, and are therefore able to support a relative abundance of functional habitats and wildlife (Source: Project Clean Water, 2005).


                           Temecula Gorge                                Near Fallbrook            Photo by Douglas Aguillard            

One of the last free flowing rivers in Southern California, the Santa Margarita River is widely recognized by various local, state and federal agencies to be an irreplaceable scenic and ecological treasure. The river's 27 miles of lush riparian vegetation is a singular natural resource in this rapidly urbanizing region. Its diversity of vegetative and aquatic habitats are home to numerous plants and animals, including 500 plant species, 236 bird species, 52 mammal species, 43 reptile species, 26 fish species and 24 species of aquatic invertebrates. 

The riparian corridor contains the highest density and overall diversity of bird species of any natural area in the south coastal river basin. The Santa Margarita's lush riparian growth supports a substantial percentage of the nation's entire population of the endangered Least Bell's Vireo. This small migratory song bird has been extirpated from 95 percent of its historic breeding range, but has found a home in the Santa Margarita River canyon. The lower portion of the river supports extensive coastal wetlands which provide important habitat for other sensitive and endangered bird species, including the Light-footed Clapper Rail, Belding's Savannah Sparrow and California Least Tern.

The Santa Margarita River also supports the largest remaining native population of Arroyo Chub, a small fish which was formerly abundant throughout Southern California. Large runs of coastal steelhead trout have been extirpated from the Santa Margarita, but the river remains one of the few nearly pristine coastal watersheds in which to reintroduce this biologically unique species (source: Friends of the River, 2005).


San Luis Rey River

The San Luis Rey (SLR) River is located primarily along Highway 76 in Oceanside. Originating in the Palomar and Hot Springs Mountains, the river ultimately ends at the Pacific Ocean. It extends over 55 miles across northern San Diego County forming a watershed with an area of approximately 360,000 acres or 562 square miles. Within the City of Oceanside, the San Luis Rey River is also fed by one of its tributaries, Pilgram Creek, which is located on the northeast end of Oceanside.


About 8 percent of the City of Oceanside’s water supply comes from the San Luis Rey River Basin. Water from the basin is pumped from wells and treated at a reverse osmosis plant before being sent to Oceanside residents.

There are 36 vegetation communities within the SLR River Watershed, with the coastal sage scrub, chaparral and grassland communities being the most abundant. Numerous protected and sensitive species and vegetation communities occur throughout the watershed.

The San Luis Rey River flows through the County of Riverside, County of San Diego, City of Escondido and City of Vista before making its way downstream to Oceanside. There are numerous land use types within the watershed; however, the majority of the watershed has remained undeveloped. Much of the western half of the watershed is privately owned and much of the eastern half is publicly owned.


San Dieguito River

The watershed extends through a diverse array of habitats from its eastern headwaters in the Volcan Mountains to the outlet at the San Dieguito Lagoon and the Pacific Ocean.  There are several important natural areas within the watershed that sustain a number of threatened and endangered species.  Among these are the 55-mile long, 80,000 acre San Dieguito River Park, the 150 acre San Dieguito Lagoon, and five water storage reservoirs including Lake Hodges, Lake Sutherland, and Lake Poway.

San Diego River

San Diego River

The five reservoirs in the San Diego River watershed supply water to as many as 760,000 residents in the region. Other areas including the Cleveland National Forest, Mission Trails Regional Park, and the river flood plain near Lakeside represent three important undeveloped areas that host a wide variety of intact habitats and endangered species like the arroyo toad, least bell’s vireo, and the southwestern pond turtle. In addition, Famosa Slough, near the mouth of the San Diego River contains extremely productive wetlands habitat.

The mouth of the river discharges into the Pacific Ocean at the community of Ocean Beach.


Sweetwater River   

Between the headwaters and the outlet to San Diego Bay, the watershed contains a variety of habitat types including oak and pine woodlands, riparian forest, chaparral, coastal sage scrub, and coastal salt marsh.  The upper watershed contains large undeveloped areas within the Cleveland National Forest and Cuyamaca Rancho State Park, the unincorporated communities of Pine Valley, Descanso, and Alpine, and the Viejas Indian Reservation.  Unincorporated rural and suburban communities characterize the central part of the watershed.  The urbanized lower portion of the Sweetwater watershed contains portions of several cities including San Diego, National City, Chula Vista, La Mesa, and Lemon Grove. 


Headwaters of the Sweewater River in Cuyamaca Rancho State Park                                                                       Photo by Barbara Barnes




Otay River

Otay dam and reservoir                                                                                                                                                     University of San Diego



Photo Credits:

Buxton, C. (2005). Photo of Cedar Creek Falls (San Diego River.) Retrieved May 2, 2005 from Friends of the River at

City of Oceanside. (2005). Photos of San Luis Rey River. Retrieved May 3, 2005 from City of Oceanside Clean Water Program at

Evans, S. (2005). Photos of Santa Margarita River. Retrieved May 2, 2005 from Friends of the River at

University of San Diego. (2005). Photo of Otay dam and reservoir. Retreived May 2, 2005 from Online Resources at the University of San Diego (Otay Valley) at