The Tijuana River watershed encompasses a region of approximately 1,750 square miles on either side of the California – Baja California border, and in terms of water quality degradation is probably the most severely impacted watershed in San Diego County.  Although only 27% of the watershed area is within California, the river discharges to the Tijuana Estuary and Pacific Ocean on the U.S. side of the international border.  On the U.S. side of the border, the cities of Imperial Beach and San Diego, and San Diego County have portions of their jurisdictions within the watershed.    The cities of Tijuana and Tecate are the most important urban centers on the Mexican side.  The current population of the entire watershed is approximately one million people.

The Tijuana River watershed is classified as a Category I (impaired) watershed by the State Water Resources Control Board due to a wide variety of water quality problems.  These problems are largely a result of non-point agricultural sources on the U.S. side of the border and a large variety of point and non-point sources on the Mexican side.  The Tijuana Estuary, a National Estuarine Sanctuary that supports a variety of threatened and endangered plants and animals, is threatened by inflows from the Tijuana River containing high concentrations of coliform bacteria, sediment, trace metals (copper, lead, zinc, chromium, nickel, and cadmium), PCBs, and other urban, agricultural, and industrial pollutants.

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

Summary of beneficial use designations.