The Los Penasquitos Hydrologic Unit (906) is comprised of the Los Penasquitos Creek watershed (906.10 - 906.20), several coastal tributaries (906.30), and the Mission Bay watershed (906.40 - 906.50).  These watersheds drain a highly urbanized region located almost entirely west of Interstate 15 in coastal San Diego County.  Collectively and individually, they support a variety of water supply, economic, recreational, and habitat-related beneficial uses.  The major receiving waters, Los Penasquitos Lagoon and Mission Bay, are both fragile systems that support diverse native fauna and flora.  Both water bodies are especially sensitive to the effects of pollutants due to restricted or intermittent tidal flushing.

The Los Penasquitos Creek watershed encompasses a land area of approximately 100 square miles including portions of the cities San Diego, Poway, and Del Mar.  The watershed is highly urbanized with a population of approximately 400,000 residents.  The creek discharges to a 0.6 square mile lagoon that is identified as an impaired water body on the California 303(d) list for sedimentation.

The Mission Bay watershed drains an area of approximately 80 square miles.  Rose Creek and Tecolote Creek are the main tributaries to the Bay, which was converted from a coastal marshland in the 1940s after the completion of a large dredging project.  Much of Mission Bay is adversely affected by coliform bacteria inputted by urban runoff and sewage spills, which are discharged by the main tributaries and smaller conveyances draining the watershed.  Tecolote Creek is identified as an impaired water body on the California 303(d) list for a host of pollutants including coliform bacteria, trace metals, and toxicity.

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