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.

Many water bodies actually support a multitude of beneficial uses, including those that directly and indirectly benefit humans. Please see table below.


64 miles2

232,000 (2010 U.S. Census)

Rose Creek, Tecolote Creek, Mission Bay, and San Diego Marine Life Refuge Area of Special Biological Significance.

Indicator bacteria, nutrients, trace metals and toxics.

  2010 Clean Water Act 303(d) List

Water Body + 303(d) List of Impairments (Condition(s)/Constituent(s))*

Eutrophic, Lead, Enterococcus, Fecal Coliform, Total Coliform
Total Coliform, Enterococcus, Fecal Coliform
Selenium, Toxicity
Cadmium, Copper, Indicator Bacteria, Lead, Nitrogen, Phosphorus, Selenium, Toxicity, Turbidity, Zinc

*CWA 303(d) listings within the Mission Bay / La Jolla Watershed as designated in the State Water Board 2010 CWA 303(d) list


The Mission Bay / La Jolla WMA contains a number of environmentally sensitive areas (ESAs), as defined in Chapter 5 of the San Diego Regional Basin Plan.

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Beneficial Uses* Inland Surface Water  Coastal Water  Reservoirs and Lakes Ground Water
 Agricultural Supply (AGR)  x x
Aquaculture (AQUA)  x
 Biological Habitats of Special Significance (BIOL)  x
 Cold Freshwater Habitat (COLD)  x  x
 Commercial and Sport Fishing (COMM)  x
 Contact Water Recreation (REC-1)  x  x  x
Hydrogen Power (POW) x
 Estuarine Habitat (EST)  x
Industrial Process Supply (PRO)
Industrial Service Supply (PROC)  x  x  x  x
Marine Habitat (MAR)  x
Migration of Aquatic Organisms (MIGR)  x
Municipal and Domestic Supply (MUN)  x  x
Navigation (NAV)  x
Non-Contact Water Recreation (REC-2)  x  x  x
Rare, Threatened, or Endangered Species (RARE)  x  x
Shellfish Harvesting (SHELL)  x
Spawning, Reproduction and/ or Early Development (SPWN)  x
Warm Freshwater Habitat (WARM)  x  x
Wildlife Habitat (WILD)  x  x  x
*Beneficial water uses within the Mission Bay / La Jolla Watershed as designated in the State Water Resources Control Board’s San Diego Region Basin Plan


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.



Scripps Hydrologic Area (906.3)

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.

What land area is covered by the Torrey Pines State National Reserve?

Miramar Hydrologic Area (906.4)

Kendall-Frost Mission Bay Marsh Preserve

Kendall-Frost Mission Bay Marsh Preserve  http://nrs.ucsd.edu/_images/homepage-rotator/kendall.png

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.

Which creek is the longest in the WMA?

Tecolote Hydrologic Area (906.5)

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.

What is the primary water body in the Tecolote Creek Hydrologic Area?


“Kendall-Frost Marsh Reserve.” Natural Reserve System – UC San Diego. UC San Diego, n.d. Web. <http://nrs.ucsd.edu/reserves/kendall.html>.

San Diego County MS4 Copermittees. 2008. Mission Bay & La Jolla Watershed Urban Runoff Management Plan (WURMP). Final, March 2008. Submitted to the San Diego Regional Water Quality Control Board by the Mission Bay & La Jolla WURMP Copermittees.

San Diego County MS4 Copermittees. 2016. Mission Bay Watershed Management Area Water Quality Improvement Plan (WQIP). Final, February 2016. Submitted to the San Diego Regional Water Quality Control Board by the Mission Bay & La Jolla Copermittees. Prepared by Amec Foster Wheeler Environment & Infrastructure, Inc. for the San Diego County MS4 Copermittees: California Department of Transportation, the City of San Diego.

San Diego Regional Water Quality Control Board (San Diego Regional Board). 2016 (August 5). Basin Plan. San Diego, CA. Available: http://www.waterboards.ca.gov/sandiego/water_issues/programs/basin_plan.

State Water Resources Control Board. 2010. California’s 2010 Clean Water Act Section 303(d) List of Water Quality Limited Segments. Approved October 11, 2011. Sacramento, CA: State Water Resources Control Board.


Your assistance is needed to develop effective strategies for improving and protecting water quality in our region’s creeks, rivers, and coastal waters!

Whether you become involved in the public process or you simply take steps to limit your own water usage in and around your home, you can become a part of the solution.

  • Think about replacing sod and other water-intensive shrubbery with drought-tolerant landscaping. As a result of the drought, many jurisdictions and water agencies actually offer rebates and other incentives to remove natural turf and install rain barrels and other water capture devices. Not only will this save you money up front, but it will also reduce your monthly water bill! Keep in mind that irrigation runoff from your property is prohibited and can result in a fine.

  • Limit car washing and power-washing of building exteriors as much as possible. If your vehicle is in need of some TLC, then consider taking it to a certified car wash. If you are on a budget, then wash your car over permeable or unpaved surfaces, allowing any excess water to be absorbed into the soil instead of running into storm drains. 

  • Dispose of pest waste appropriately. When taking your dog for a walk, make sure that you always have a bag on hand so that when nature calls, you are ready. This will help prevent bacteria and pathogens that can cause illness from getting into our waterways.

  • If you have some free time and don’t mind getting your hands a little dirty, many conservancies and foundations host clean up events for local creeks and lagoons. Please see our calendar to learn more about what events are being offered in your area!

  • Don’t litter! Trash on our roadways and in our yards has a tendency to make its way to creeks, rivers, and ocean waters during rain events. Even consider carrying a bag with you to collect litter as you take your morning or evening neighborhood stroll.

  • Implementation and adaptation of the Water Quality Improvement Plan is an ongoing process and as always, public input is encouraged. Meetings that are open to the public are posted in a timely manner to allow for public involvement. If you are interested, please check out our calendar for upcoming meetings.

  • If you observe any discharges of water that you believe may be illicit, then do not hesitate to report it by means of our pollution reporting page.

  • And lastly, do what you can to spread the word! Sometimes the most effective strategy is the simplest one. Now that you are a water quality expert, we are relying on your help to educate your coworkers, family, and friends.