The Carlsbad Hydrologic Unit (HU) is approximately 210 square miles in area extending from the headwaters above Lake Wolhford in the east to the Pacific Ocean in the west, and from Vista and Oceanside in the north to Solana Beach, Escondido, and the community of Rancho Santa Fe to the south.  The cities of Carlsbad, San Marcos, and Encinitas are entirely within this HU.  There are numerous important surface hydrologic features within the Carlsbad HU including four unique coastal lagoons, three major creeks, and two large water storage reservoirs.  The HU contains four major, roughly parallel hydrologic areas (HAs).  From north to south they are the Buena Vista (901.2), the Agua Hedionda (904.3), the Batiquitos (904.5), and the San Elijo (904.6) HAs.   Two smaller HAs, the Loma Alta (904.1) and the Canyon de las Encinas (904.4) are also within the Carlsbad HU.

The largest jurisdictions in terms of land area in the Carlsbad HU are the unincorporated San Diego County areas (66 sq. miles), the cities of Carlsbad (39 sq. miles) and San Marcos (24 sq. miles), and an approximately 27 square mile portion of the City of Escondido.  The cities of Carlsbad, San Marcos, and Encinitas are located entirely within the HU.  Approximately 48% of the Carlsbad HU is urbanized.  The dominant land uses are residential (29%), commercial/industrial (6%), freeways and roads (12%), agriculture (12%), and vacant/undeveloped (32%). 

The Agua Hedionda, Buena Vista, and San Elijo lagoons are experiencing impairments to beneficial uses due to excessive coliform bacteria and sediment loading from upstream sources.  These coastal lagoons represent critical regional resources that provide freshwater and estuarine habitats for numerous plant and animal species.   Other water bodies in the Carlsbad HU have been identified as impaired on the California 303(d) list for elevated coliform bacteria including several locations in the Pacific Ocean near creek and lagoon outlets.

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