Santa Margarita Topography

The San Diego River Watershed encompasses a land area of 434 square miles, making it the second largest watershed management area (WMA) located in San Diego County. It lies in the central portion of the County and neighbors Los Penasquitos and San Dieguito River Watersheds to the north and San Diego Bay WMA to the south.

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

  • Lower San Diego (907.1)
  • San Vicente (907.2)
  • El Capitan (907.3)
  • Boulder Creek (907.4)

Rainfall to the area primarily drains through the San Diego River, which stretches east to west over a distance of roughly fifty-two (52) miles and originates near Santa Ysabel, in the Cuyamaca Mountains. The river eventually discharges to the Pacific Ocean near the community of Ocean Beach.

Currently, about forty-four percent (44%) of the watershed management area (WMA) remains undeveloped. The remaining fifty-six percent (56%) of the land area is being utilized for open space and park land (23%), residential areas (19%), transportation (6%), and other (2%). The remaining ‘other’ two percent (2%) includes commercial, agricultural, industrial, military, and miscellaneous land uses. To see a more detailed breakdown of land uses by hydrologic area, please see Lower San Diego, San Vicente, El Capitan, and Boulder Creek Hydrologic Area descriptions below.

The most populous WMA in San Diego County, the San Diego River Watershed is estimated to be home to approximately 520,000 residents, according to 2010 US Census data. The vast majority of the population is concentrated 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. 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.

San Diego River Watershed supplies roughly 760,000 individuals with potable water sourced from one of five reservoirs: Lake Murray, Lake Jennings, San Vicente, El Capitan and Cuyamaca Reservoirs. The majority of these reservoirs can be found in the eastern half of the watershed, upstream from the Lower San Diego Hydrologic Area.

It is important to note, however, that the watershed serves more than just humans. The San Diego River Watershed consists of a variety of unique and diverse ecosystems that act as critical habitat for a number of endangered species, including the arroyo toad, least bell’s vireo, and the southwestern pond turtle.

Furthermore, many of the water bodies support a number of beneficial uses as shown in the table below.


434 miles2

520,000 (2010 U.S. Census)
San Diego River, El Capitan Reservoir, San Vincente Reservoir, Lake Murray, Boulder Creek, Santee Lakes.
Coliform bacteria, total dissolved solids (TDS), nutrients, petroleum chemicals, toxics, and trash.

  2010 Clean Water Act 303(d) List

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

Color, Manganese, Phosphorus, Total Nitrogen as N, pH
Fecal Coliform, Selenium, TDS, pH
Enterococcus, Fecal Coliform, Dissolved Oxygen, Manganese, Nitrogen, Phosphorus, TDS, Aquatic Toxicity
Enterococcus, Fecal Coliform, Total Coliform, Copper
Nitrogen, pH
Enterococcus, Total Coliform
Ammonia as Nitrogen, Benthic Community Effects, Total Nitrogen as N, Aquatic Toxicity
Chloride, Color, Sulfates, Total Nitrogen as N, pH (high)

*CWA 303(d) listings within the San Diego River WMA as designated in the State Water Board 2010 CWA 303(d) list


The San Diego River 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
 Estuarine Habitat (EST)  x
Hydropower Generation (POW) x
Industrial Process Supply (PRO)  x  x  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  x
Navigation (NAV)  x
Non-Contact Water Recreation (REC-2)  x  x  x
Rare, Threatened, or Endangered Species (RARE)  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 San Diego River WMA 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. Sources of pollutants within the San Diego River Watershed include urban and agricultural runoff, mining operations, and sewage spills.

Under Section 303(d) of the Clean Water Act, the Lower San Diego River Watershed was identified as impaired for coliform bacteria. This condition 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)) to the National Pollutant Discharge Elimination System (NPDES) Permit focus their treatment and cleanup efforts on this particular water quality condition.

As part of the process, however, 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 San Diego River WMA, copermittees include the County of San Diego and the Cities of San Diego, El Cajon, La Mesa, Poway, and Santee. The WQIP for the San Diego River WMA was submitted and received approval from the Regional Water Quality Control Board in February 2016. Copermittees within the San Diego River WMA selected bacteria in the Lower San Diego River Watershed as their highest priority water quality condition.



Lower San Diego Hydrologic Area (907.1)

Of the HAs located within the San Diego River Watershed, the Lower San Diego Hydrologic Area (907.1) is the most urbanized and suffers from the most pronounced water quality problems. At roughly 110,000 acres, it is also the largest and represents approximately forty percent (40%) of the watershed. Due to its geographic extent, oversight of the storm drain systems within the Lower San Diego Hydrologic Area falls on a number of copermittees: namely, the County of San Diego in combination with the Cities of Santee, El Cajon, La Mesa, and San Diego.

Typically, surface runoff within the basin drains into the San Diego River and is subsequently discharged directly into the Pacific Ocean at Ocean Beach. At the point where the San Diego River meets the Pacific Ocean lies a 37 acre wetland, Famosa Slough, which is managed by the City of San Diego. In addition, the Lower San Diego Hydrologic Area is home to Lake Murray, one of a few major reservoirs within the San Diego River WMA.

The Lower San Diego Hydrologic Area is significantly more developed than its counterparts upstream. Here, undeveloped and open lands make up roughly forty-three percent (43%) of the land area, followed closely by residential uses at thirty percent (30%).

Due to extensive anthropogenic modifications to the environment associated with urbanization, several native plant and animal species commonly found in the Lower San Diego Hydrologic Area have been put at risk of endangerment. A number of threatened and endangered species have been observed here, including the coastal California condor, the great grey owl, the horned lizard, and the kangaroo rat.

The Lower San Diego system consists of a number of water bodies that are listed as impaired under Section 303(d) of the Clean Water Act. Several of the water bodies listed as impaired include Alvarado Creek, Lower San Diego River, Forester Creek, and Lake Murray. These water bodies are impacted by pollutants such as fecal coliform, enterococcus, selenium, nitrogen, manganese, phosphorus, total dissolved solids, and low dissolved oxygen.

Which community is closest to the point at which the San Diego River meets the Pacific Ocean?

San Vicente Hydrologic Area (907.2)

At roughly 47,000 acres, the San Vicente Hydrologic Area is the smallest drainage basin within the San Diego River WMA and has a considerable share of undeveloped land. With the exception of some Native American tribal lands, the entirety of the San Vicente Hydrologic Area lies within the jurisdiction of the County of San Diego.

All of the surface water here flows into and is impounded within San Vicente Reservoir. However, underground aquifers also contribute significantly to the local water supply. Water agency supply records and population data indicate that hundreds of private groundwater wells exist in the San Vicente Hydrologic Area alone.

In recent years, the San Vicente sub-watershed has seen continued human expansion that exerts increasing pressure on the surrounding habitat and ecosystems. Some examples of threatened and endangered species that are known to occur in the San Vicente Hydrologic Area are the Encinitas baccharis, the arroyo toad, and the bald eagle.

Land uses in this portion of the WMA tend to be more variable that in other areas. One of the most recent figures estimates that the San Vicente HA is made up primarily of lands that are undeveloped or open spaces, at sixty-five percent (65%) of the total area. Residential land uses follow, constituting approximately sixteen percent (16%) of the HA. A portion of the sub-watershed is also allocated Native American Reservation land and lies outside of the jurisdiction of typical copermittees.

The San Vicente sub-watershed is home to a couple of water bodies that are listed as impaired under Section 303(d) of the Clean Water Act. For example, San Vicente Creek and San Vicente Reservoir have been listed as impacted by a number of pollutants, including nitrogen, chloride, sulfates, and elevated aquatic toxicity and pH levels.

What threatened and endangered species have been observed in the San Vicente Hydrologic Area?

El Capitan Hydrologic Area (907.3)

El Capitan Hydrologic Area is located just south of the Boulder Creek and San Vicente Hydrologic Areas and covers a land area of about 56,000 acres. It lies primarily within the jurisdiction of the County of San Diego; however, the portion of the sub-watershed within the Capitan Grande Reservation is outside of the jurisdiction of the County of San Diego.

The hydrologic area receives significant runoff from the community of Alpine through Chocolate and Peutz Valley Creeks. All surface runoff, however, is eventually directed into El Capitan Reservoir, a water body that was created by damming San Vicente Creek in 1935. Prior to completion of the San Vicente Dam Raise Project in 2015, El Capitan Reservoir had the greatest storage capacity of any reservoir in the City of San Diego reservoir system. In order to satisfy demand, reservoir supplies are supplemented by groundwater sourced from local aquifers.

Like its neighbor hydrologic areas, the El Capitan system contains vast tracts of undeveloped land, including portions of the Cleveland National Forest. In fact, about eighty-seven percent (87%) of its land area is currently undeveloped land or open space, and only nine percent (9%) of the hydrologic area is being utilized for residential land uses. The remaining land area is divided between other miscellaneous uses.

Unfortunately, El Capitan Lake has been identified under Section 303(d) of the Clean Water Act as impaired for pollutants including manganese, phosphorus, nitrogen, and pH. Urban runoff is considered the most substantial contributor of many of these constituents.

When was El Capitan Reservoir established?

Boulder Creek Hydrologic Area (907.4)

Known as the headwaters, the Boulder Creek Hydrologic Area begins with William Heise County Park and Cuyamaca Rancho State Park in the east and extends westward to encompass a region of approximately 63,000 acres. Although the County of San Diego has been identified as the only copermittee within the hydrologic area, the Inaja and Cosmit Indian Reservation constitutes a large part of the basin. As federal lands, however, the Reservation is not subject to the same requirements as those lands under County jurisdiction.

Primary water bodies in the system include Boulder Creek and Cuyamaca Reservoir, a lake located near the eastern border of the WMA. Almost all water in the Boulder Creek Hydrologic Area originates from the melting of seasonal snow cover. As such, the flow rate of creeks and rivers in the system and downstream varies immensely depending upon the season. Low-flow conditions in the system typically occur from October to March. High-flow conditions, on the other hand, generally occur between May and July, peaking in June. These waters typically have very low concentrations of dissolved solids, alkalinity, and nutrients compared to downstream waters. Surface waters frequently have near-neutral pH values, and dissolved oxygen is at or near saturation.

Encompassing large tracts of the Cleveland National Forest, land use is in the hydrologic area is dominated principally by undeveloped lands and open space, making up about eighty-eight percent (88%) of the sub-watershed area. The remainder of the land is distributed between residential uses (7%), agricultural uses (3%), and other uses.

Experiencing minimal effects on water quality due to development, water bodies within this region of the management area have largely escaped water quality issues that are more prevalent in portions of the watershed downstream.

Which Reservation is located within the Boulder Creek Hydrologic Area?


“El Capitan Reservoir.” The City of San Diego. The City of San Diego, n.d. Web. <>.

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

San Diego County MS4 Copermittees. 2016. San Diego River Watershed Management Area Water Quality Improvement Plan (WQIP). Final, January 2016. Submitted to the San Diego Regional Water Quality Control Board by the San Diego River Copermittees. Prepared by Larry Walker and Associates and Amec Foster Wheeler Environment & Infrastructure, Inc. for the San Diego County MS4 Copermittees: California Department of Transportation, City of El Cajon, City of La Mesa, City of San Diego, City of Santee, County of San Diego.

San Diego Regional Water Quality Control Board (San Diego Regional Board). 2016 (August 5). Basin Plan. San Diego, CA. Available:

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.