The Sweetwater River watershed along with the Otay and Pueblo San Diego watersheds combine to form the San Diego Bay watershed area.  The Sweetwater River watershed is the largest of the three encompassing 230 of the approximately 415 square mile total.  Over 86% of the watershed is within unincorporated jurisdictions.  The dominant land uses in the Sweetwater River watershed are urban (29%), open space/ agriculture (22%), and undeveloped (49%).  Approximately two-thirds of the land area categorized as urban is composed of residential communities.  Approximately 300,000 people currently reside within the Sweetwater River watershed, and this amount is projected to increase to 365,000 by 2015.  The most important watershed issues are related to the protection of municipal water supplies, and the protection and restoration of sensitive wetland and wildlife habitats.

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.  Of the cities within the watershed, Chula Vista is the most important in terms of land area.

There are many beneficial water uses within the Sweetwater Watershed as designated in the State Water Resources Control Board's San Diego Region Basin Plan.