The Otay River watershed encompasses approximately 160 square miles in southwest San Diego County and is one of the three hydrologic units that discharge to San Diego Bay.  The watershed consists largely of unincorporated area, but also includes portions of the cities of Chula Vista, Imperial Beach, Coronado, National City, and San Diego.  The predominant land uses in the watershed are open space (67%) and urban/residential (20%). The major inland hydrologic features, Upper and Lower Otay Lakes, are two water supply reservoirs that also provide important habitat and recreational opportunities.  Approximately 36 square miles of the watershed is part of the Multiple Species Conservation Plan effort that provides habitat for a wide range of endangered plant and animal species.  Other important conservation areas within the watershed include the San Diego National Wildlife Refuge, the Rancho Jamul Ecological Reserve, and the vernal pool lands in the region.

The current population in the Otay River watershed is approximately 150,000 people.  At the present time, serious water quality problems are limited to the presence of elevated coliform bacteria in the Pacific Ocean receiving waters near Coronado.  However, an expected population increase of 88% from 1998 – 2015 will substantially increase the volume of urban runoff in the watershed, and could significantly alter the present water quality status.  In the absence of effective watershed-based management, the natural resources of the Otay River watershed may be significantly degraded.

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