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Mission Bay / La Jolla

Watershed Management Area (WMA)

Photography By: Brianna Martin, Francesca DeLeon and Minell Enslin.


Santa Margarita Topography

The Mission Bay and La Jolla Watershed Management Area (WMA) encompasses a land area of only sixty-four (64) square miles, making it the smallest WMA in San Diego County. It lies in the central portion of the County and neighbors Los Penasquitos WMA to the north and San Diego River Watershed to the south.

Typically assumed to work in conjunction with the Los Penasquitos WMA to form one fully functional watershed, the Mission Bay and La Jolla WMA has a slightly different set of priorities and is therefore considered separate for the purposes of this summary.

The WMA can be divided into three distinct hydrological areas, each with unique geological and environmental features:

  • Scripps (906.3)
  • Miramar (906.4)
  • Tecolote (906.5)

Rainfall to the area primarily drains through Rose and Tecolote Creeks, each of which discharges into Mission Bay before the water is subsequently directed into the Pacific Ocean. Cudahy Creek is another tributary crucial to the WMA.

Currently, about thirty-seven percent (37%) of the WMA remains undeveloped or has otherwise been dedicated to open space and recreational lands. The remaining sixty-three percent (63%) of the land area is being utilized as residential areas (28%), roadways and transportation (16%), office and institutional lands (7%), and other (12%). The remaining ‘other’ twelve percent (12%) includes industrial, commercial, and agricultural land uses.

The Mission Bay and La Jolla WMA is estimated to be home to approximately 232,000 residents, according to 2010 U.S. Census data. Given its dense population, the watershed suffers from several human-induced pollutants, which have the potential to negatively impact how residents, business-owners, and tourists use and interact with local water bodies. It is important to note, however, that the watershed serves more than just humans.

The Mission Bay and La Jolla WMA consists of a variety of unique and diverse ecosystems that also act as critical habitat for a number of endangered species.

For more information about water bodies see the San Diego Basin Plan, which provides information on uses of water bodies and water quality objectives, beneficial uses and the 303(d) list, which identifies water body segments not meeting water quality standards.

Water Quality Improvement Plan (WQIP)

  • Mission Bay / La Jolla (MSB) Water Quality Improvement Plan (WQIP)

Agencies involved in the development of the Mission Bay/La Jolla Water Quality Improvement Plan (WQIP) include the City of San Diego and the California Department of Transportation. The WQIP is a requirement of updated stormwater regulations adopted by the Regional Water Quality Control Board (Regional Board) according to Order No. R9-2013-0001, as amended by Order Nos. R9 2015-0001 and R9-2015-0100. The ultimate goal of the WQIP is to protect, preserve, enhance, and restore water quality of receiving water bodies. These improvements in water quality will be accomplished through an adaptive planning and management process that identifies the highest priority water quality conditions within the watershed and implements strategies to address them.

The Mission Bay/La Jolla Water Quality Improvement Plan was originally submitted to the Regional Board on June 26, 2015, as required by the Municipal Permit. The WQIP was subsequently revised and resubmitted in order to incorporate comments received from the public and the Regional Board. Following further comments, the Regional Board issued an acceptance letter for the Mission Bay/La Jolla WQIP on February 12, 2016. The resulting WQIP, appendices, and acceptance letter are available at the links above.

WQIP Annual Reports

The Mission Bay / La Jolla Management Area (WMA) Water Quality Improvement Plan (WQIP) Annual Reports allow copermittees to demonstrate progress made during the fiscal year towards achieving water quality goals. They are a direct requirement of the National Pollutant Discharge Elimination System (NPDES) Permit, Order No. R9-2013-0001, as amended by Order Nos. R9-2015-0001 and R9-2015-0100. The Annual Reports contain specific information regarding strategy implementation and monitoring efforts and data. Furthermore, they serve as a basis upon which copermittees may choose to adaptively manage their highest priorities and goals/strategies, according to the most recent water quality data.

For most San Diego Region watersheds, FY 2015-16 is the first year of WQIP implementation and is therefore the first year of annual reporting. Annual reports are submitted to the Regional Board by January 31 of the following year.

Below are the most recent annual reports, to view years prior to 2015-2016 click here.

  • FY 2018-2019 Mission Bay/La Jolla WQIP Annual Report and Appendices
  • FY 2017-18 Mission Bay/La Jolla WQIP Annual Report and Appendices
  • FY 2016-17 Mission Bay/La Jolla WQIP Annual Report and Appendices
  • FY 2015-16 Mission Bay/La Jolla WQIP Annual Report and Appendices

Other Plans and Projects

Additional plans and projects not necessarily associated with the Water Quality Improvement Plan (WQIP) are listed below.

Transitional Monitoring and Assessment Program Report (TMAR)

A requirement of the Municipal Permit Order No. 2013-0001 (as amended in Order Nos. R9-2015-0001 and R9-2015-0100), transitional monitoring was conducted and reported on prior to development of the Mission Bay / La Jolla WQIP. The reports, appendices, and associated documents can be found below:

  • Mission Bay / La Jolla (MSB) Transitional Monitoring and Assessment Program Report (TMAR)

Things To Consider

When excessive quantities of pollutants are deposited into these water bodies, they may inhibit many or all of these beneficial uses, which can result in actions such as beach closures and postings, etc. Urban runoff, sewage spills, dredging, and landfill leachate are considered the major sources impacting the above beneficial uses in the Mission Bay WMA.

Under Section 303(d) of the Clean Water Act, Tecolote Creek and the Pacific Ocean Shoreline were identified as impaired for coliform bacteria, which is required to be addressed through a number of best management practices and regular monitoring. As such, copermittees (also referred to as Responsible Agencies (RAs)) focus their treatment and cleanup efforts on this particular water quality condition.

Copermittees are required to develop a comprehensive Water Quality Improvement Plan (WQIP) for the WMA that identifies highest priority water quality conditions, strategies to address them, and monitoring plans. The WQIP and associated Annual Reports are required by Order No. R9-2013-0001 as amended by Order Nos. R9-2015-0001 and R9-2015-0100 and pertain specifically to improving the quality of both storm water and non-storm water discharged by copermittees’ municipal separate storm sewer systems (MS4s).

In the Mission Bay WMA, the City of San Diego is the sole permittee; however, the City collaborates with Caltrans in implementing the WQIP. The final WQIP for the San Luis Rey WMA was submitted to the Regional Water Quality Control Board and was accepted in February 2016. The City of San Diego has chosen to focus their treatment and cleanup efforts on indicator bacteria in Tecolote Creek and the Pacific Ocean Shoreline, conditions which has been classified as the highest priority water quality condition.

Click here for education and outreach information.

Hydrologic Area (HA) Descriptions

Scripps HA (906.3)

La Jolla Cove –

The Scripps Hydrologic Area consists of about 6,600 acres in and around the La Jolla peninsula. The region lies completely within the jurisdiction of the City of San Diego, meaning that it puts forth the majority of monitoring efforts to reduce and eliminate non-storm water flows and potential contaminants from entering the area’s municipal separate storm and sewer system.

Located partially within the Scripps Hydrologic Area and partially within the Los Penasquitos WMA, Torrey Pines State National Reserve contains about 2,000 acres of protected lands. This designation acknowledges the area’s biodiversity and calls for more limited human presence as compared to that which would be permissible in a National Park.

Nevertheless, the area is relatively urbanized, with open space and undeveloped land comprising just twenty-six percent (26%) of the hydrologic area. Here, residential uses remain at the forefront, constituting nearly fifty percent (46%) of the land area. Roadways and miscellaneous transportation uses follow at approximately nineteen percent (19%).

Similar to other watersheds, the Mission Bay WMA has been listed as impaired under Section 303(d) of the Clean Water Act at the Pacific Ocean Shoreline. Here, coastal waters are primarily impacted by coliform bacteria and enterococcus.

Miramar HA (906.4)

Kendall-Frost Mission Bay Marsh Preserve –

The largest of the Mission Bay hydrologic areas, the Miramar Hydrologic Area encompasses nearly 28,000 acres of land and much like the Scripps Hydrologic Area, lies completely within the jurisdiction of the City of San Diego.

In addition to Rose Creek, the Miramar system also encompasses San Clemente Creek, the longest creek in the WMA. These two creeks redirect the vast majority of the watershed’s surface runoff towards Mission Bay and the Pacific Ocean. Along the northern edge of Mission Bay are two areas specially designated as sensitive: the Kendall-Frost Mission Bay Marsh Reserve and Northern Wildlife Preserve, which together protect approximately forty (40) acres of tidal wetlands that are home to California least terns, light-footed clapper rails, and Belding’s savannah sparrows.

Here, open spaces and undeveloped lands dominate, making up forty-four percent (44%) of the drainage basin’s total land area. Residential lands constitute twenty-one percent (21%) of the area, followed closely by transportation at eighteen percent (18%) of land area.

Within the Miramar Hydrologic Area, several water bodies have been listed as impaired under Section 303(d) of the Clean Water Act. Rose Creek, for example, has been listed as being impacted by selenium and aquatic toxicity. Similarly, Mission Bay suffers from occasional eutrophic conditions and high levels of lead, enterococcus, fecal coliform bacteria, and total coliform bacteria.

Tecolote HA (906.5)

Tecolote Canyon Natural Park –

The southernmost system within the WMA, the Tecolote Hydrologic Area contains portions of Mission Bay in addition to about 9,000 acres of land. Here, the sole jurisdiction is the City of San Diego; however, its efforts are complemented by those made by Caltrans to help improve water quality conditions in receiving waters.

Bisecting Tecolote Canyon Natural Park is Tecolote Creek, which is the primary water body in the hydrologic area and discharges to Mission Bay. Tecolote Natural Park contains a number of hiking trails and other recreational opportunities available to the general public.

The Tecolote Hydrologic Area is the most urbanized of the Mission Bay and La Jolla hydrologic areas, with only about eighteen percent (18%) of its land area designated as open space and park lands or lands that are otherwise undeveloped. Residential is the primary land use within the hydrologic area, comprising about thirty-seven percent (37%) of the total land area, followed by transportation at twenty-two percent (22%). Other uses include lands dedicated to industrial, commercial, and miscellaneous uses.

Having experienced substantial levels of development, Tecolote Creek and Mission Bay both suffer from impairments warranting placement on the Section 303(d) list of the Clean Water Act. Tecolote Creek is affected by aquatic toxicity, turbidity, and elevated levels of cadmium, copper, indicator bacteria, lead, nitrogen, phosphorus, selenium, and zinc. Mission Bay is affected by occasional eutrophic conditions and high concentrations of lead, enterococcus, and total coliform.