With a land area of approximately 440 square miles, the San Diego River watershed is the second largest hydrologic unit (HU) in San Diego County. It also has the highest population (~475,000) of the County’s watersheds and contains portions of the cities of San Diego, El Cajon, La Mesa, Poway, and Santee and several unincorporated jurisdictions. Important hydrologic resources in the watershed include five water storage reservoirs, a large groundwater aquifer, extensive riparian habitat, coastal wetlands, and tide pools. Approximately 58.4% of the San Diego River watershed is currently undeveloped. The majority of this undeveloped land is in the upper, eastern portion of the watershed, while the lower reaches are more highly urbanized with residential (14.9%), freeways and roads (5.5%), and commercial/ industrial (4.2%) land uses predominating.

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. Beach postings and closures from elevated levels of coliform bacteria more than doubled between 1996 and 1999 due to urban runoff and sewage spills. Discharge from the San Diego River outlet may also influence water quality in other nearby coastal areas including Sunset Cliffs, Pacific Beach, and Mission Beach. The extensive groundwater resources beneath the San Diego River provide a cost effective and reliable water supply to four local water districts and the City of San Diego. Excessive extraction, increasing total dissolved solids, and MTBE contamination now threatens this resource.

Beneficial water uses within the San Diego River Watershed as designated in the State Water Resources Control Board's San Diego Region Basin Plan.

 Summary of beneficial use designations.