The San Juan Hydrologic Unit (SJHU) covers 496 square miles in San Diego, Orange, and Riverside counties.  Approximately 150 square miles (30%) of this area is located in northwest San Diego County, almost entirely within the Camp Pendleton Marine Corps Base.  There are five hydrologic areas (HA) in the SJHU, two of which, the San Onofre and San Mateo HAs are within San Diego County.  The major stream systems in the San Onofre HA drain the San Onofre, Las Flores, and Aliso Canyon basins.  It is not unusual for these creeks to be dry from July through November.  The topography of the San Onofre and San Mateo HAs is varied, ranging from coastal plains in the western portion to the Santa Margarita Mountains, which rise over 2,000 feet above mean sea level.

The San Onofre and San Mateo HAs are largely undeveloped and contain 21 recognized plant communities within the Camp Pendleton MCB including coastal sage scrub, oak woodlands, chaparral, grasslands, coastal dunes, salt marshes, and riparian woodlands.  This series of habitats supports 18 threatened or endangered plant and animal species.  Various wildlife species use the undeveloped, low-lying creeks and streambeds as corridors to range freely within the MCB and outward to surrounding open space areas like the Cleveland National Forest to the northeast.

The land uses within the San Onofre and San Mateo HAs include open space, military base operations, and agriculture.  In addition, there is a state beach along the Interstate 5 corridor near the northern boundary of the MCB, and a golf course near the southern boundary.  Nearby jurisdictions include the cities of Oceanside and San Clemente to the south and north, respectively and the community of Fallbrook to the east.   Past water quality monitoring has indicated that the region’s surface waters are high in total dissolved solids.  Local wells are the sole water source for Camp Pendleton and several elevated constituents have been noted including nitrates, TDS, iron, sodium, and E. Coli, although there appear to be no long-term trends.

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