Santa Margarita Topography

The Los Peñasquitos Watershed Management Area (WMA) encompasses a land area of 94 square miles, making it the second smallest WMA in San Diego County. It lies in the central portion of San Diego County and neighbors the San Dieguito River Watershed to the north and the Mission Bay/La Jolla and San Diego River WMAs to the south.

Functionally, the Los Peñasquitos WMA works in conjunction with the Mission Bay/La Jolla WMA to form a single hydrologic unit, or watershed. For the purposes of this summary, however, they will be considered distinct entities.

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

  • Los Peñasquitos (906.1)
  • Poway (906.2)

Rainfall to the area primarily drains through Los Peñasquitos Creek, which stretches east to west and originates near the City of Poway. The creek eventually discharges to the Pacific Ocean near the community of Del Mar at the Los Peñasquitos Lagoon. The WMA also supplies locals with potable water sourced from Miramar Reservoir, owned and operated by the City of San Diego.

Currently, about forty-six percent (46%) of the WMA remains undeveloped or has otherwise been dedicated to open space and recreational lands. The remaining fifty-four percent (54%) of the land area is being utilized as residential areas (27%), roadways and transportation (12%), and other uses (15%). The remaining ‘other’ fifteen percent (15%) includes industrial, office, commercial, and agricultural land uses. For more detailed breakdowns by hydrologic area, please see the Los Peñasquitos and Poway Hydrologic Area sections below.

According to 2010 U.S. Census data, the Los Peñasquitos WMA is estimated to be home to approximately 260,000 residents. The population is most dense in the more developed urban and suburban regions of the lower watershed, which bears a disproportionate share of the pollution burden when compared to portions of the watershed upstream. As such, the watershed suffers from several 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 Los Peñasquitos Watershed consists of a variety of unique and diverse ecosystems that act as critical habitat for a number of endangered species.

In fact, many of the water bodies in the Los Peñasquitos Watershed support multiple beneficial uses, including those in the table below.


94 miles2

260,000 (2010 U.S. Census)

Los Penasquitos Creek, Los Penasquitos Lagoon, Miramar Reservoir

Indicator bacteria, nutrients, trace metals, toxics, and sediment.

  2010 Clean Water Act 303(d) List

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

Enterococcus, Fecal Coliform, Selenium, TDS, Total Nitrogen as N, Toxicity
Sedimentation, Siltation
Total Nitrogen as N
Selenium, Toxicity
Sediment Toxicity, Selenium

*CWA 303(d) listings within the Los Penasquitos Watershed as designated in the State Water Board 2010 CWA 303(d) list


The Los Penasquitos Watershed 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
 Estuarine Habitat (EST)  x
Hydrogen Generation (POW)  x
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 Santa Margarita 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 and can result in actions such as beach closures and postings, etc. Within the Los Peñasquitos WMA, these pollutants are sourced primarily from urban runoff, sewage spills, dredging, and landfill leachate.

Under Section 303(d) of the Clean Water Act, the Pacific Ocean Shoreline was identified as impaired for indicator bacteria, which is required to be addressed through a number of best management practices and regular monitoring. Sedimentation and siltation also poses a problem for the lagoon. 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. In the Los Peñasquitos WMA, copermittees include the County of San Diego and the Cities of San Diego, Del Mar, and Poway.

Additionally, these agencies collaborate with Caltrans in implementing the WQIP. The final WQIP for the Los Peñasquitos WMA was submitted to the Regional Water Quality Control Board and was accepted in February 2016. Copermittees have chosen to focus their treatment and cleanup efforts on bacteria along the Pacific Coast Shoreline and siltation and sedimentation in Los Peñasquitos Lagoon, conditions which have been classified as highest priority water quality conditions.



Los Peñasquitos Hydrologic Area (906.1)

Discharging just south of the City of Del Mar, the Los Peñasquitos Hydrologic Area encompasses a land area of about 33,000 acres. Most of this region lies within the jurisdiction of the City of San Diego, with remaining portions of the system divided up between the City of Del Mar and San Diego County.

The system includes a number of noteworthy water bodies, such as Los Peñasquitos Creek, Carmel Valley Creek, and Carroll Canyon Creek, all of which feed into Los Peñasquitos Lagoon. Marking the point at which Los Penasquitos Creek meets the Pacific Ocean, Los Peñasquitos Lagoon is comprised of a range of ecologically and environmentally sensitive areas. For example, it is home to the Los Peñasquitos Marsh Natural Preserve, a portion of the Torrey Pines State Natural Reserve that is closed to boating and is open to hikers only on a limited basis. Much like other Southern California estuaries and lagoons, it provides habitat to a number of endangered species, largely of the avian variety.

In the upper reaches of the system, just below the Poway Hydrologic Area, is Miramar Reservoir. Completed as a part of the City of San Diego’s Aqueduct project in 1960, the reservoir has a maximum storage capacity of about 7,000 cubic acre-feet and contains water sourced from the Colorado River and California Aqueducts.1

The Los Peñasquitos system contains relatively large swaths of undeveloped land. In fact, about forty-one percent (41%) of its land area is currently undeveloped or open space, and about twenty-six percent (26%) of the hydrologic area is being utilized for residential land uses. The remaining land area is divided between transportation (15%), industrial (10%), and miscellaneous land uses (8%).

Partially as a result of development, several water bodies were listed as impaired as required by Section 303(d) of the Clean Water Act. In the Los Peñasquitos Hydrologic Area, Los Peñasquitos Creek was listed as impacted by Enterococcus bacteria, fecal coliform bacteria, selenium, total dissolved solids, total nitrogen as N, and aquatic toxicity. In addition, the lagoon is affected by sedimentation and siltation.

The Los Peñasquitos Marsh Natural Preserve is a part of what larger reserve?

Poway Hydrologic Area (906.2)

Beginning in the rolling hills just east of the City of Poway and stretching westward, the Poway Hydrologic Area covers a land area of approximately 27,000 acres. Copermittees include the County of San Diego and the Cities of San Diego and Poway.

The majority of surface runoff in the Poway Hydrologic Area is eventually directed into Los Peñasquitos Creek by way of a number of smaller creeks and tributaries. Los Peñasquitos Creek then makes its way through the Los Peñasquitos Lagoon before being discharged into the Pacific Ocean.

Land uses in this portion of the WMA tend to be more variable than in the Los Peñasquitos Hydrologic Area. One of the most recent figures estimates that the Poway Hydrologic Area is fairly evenly divided between residential land uses (33%), open spaces and undeveloped lands (27%), and miscellaneous uses (40%). The forty percent (40%) comprising the miscellaneous uses includes lands utilized for roadways and transportation (10%), industrial and commercial lands, office space, etc.

A single water body in the Poway Hydrologic Area, Poway Creek, has been listed as impaired under Section (303)d of the Clean Water Act for high levels of selenium and aquatic toxicity. These issues are currently being addressed by copermittees through a number of best management practices (BMPs).

What is the main water body in the Poway Hydrologic Area?


San Diego County MS4 Copermittees. 2008. Los Penasquitos Watershed Urban Runoff Management Program (WURMP). Final, March 2008. Submitted to the San Diego Regional Water Quality Control Board by the Los Penasquitos WURMP Copermittees.

San Diego County MS4 Copermittees, 2016. Los Penasquitos Watershed Management Area Water Quality Improvement Plan (WQIP). Final, September 2015. Submitted to the San Diego Regional Water Quality Control Board by the Los Penasquitos Copermittees. Prepared by Amec Foster Wheeler Environment & Infrastructure, Inc. for the San Diego County MS4 Copermittees: California Department of Transportation, City of Del Mar, City of Poway, City of San Diego, and County of San Diego.

San Diego County Water Authority. “Reservoirs.” San Diego County Water Authority, 24 Oct. 2016. Web. <http://www.sdcwa.org/reservoirs>.

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.