Santa Margarita Topography

The San Dieguito River Watershed Management Area (WMA) is a drainage area that encompasses approximately 345 square miles, including portions of the Cities of Del Mar, Escondido, Poway, San Diego, and Solana Beach, and unincorporated areas of San Diego County. It lies in the west-central portion of the County and neighbors Carlsbad and San Luis Rey Watersheds to the north and Los Penasquitos and San Diego River Watersheds to the south.

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

  • Solana Beach (905.1)
  • Hodges (905.2)
  • San Pasqual (905.3)
  • Santa Maria Valley (905.4)
  • Santa Ysabel (905.5)

Rainfall to the area primarily drains through the San Dieguito River, which stretches east to west and originates near Santa Ysabel, in the Cuyamaca Mountains. The river eventually discharges to the Pacific Ocean near the communities of Del Mar and Solana Beach.

The San Dieguito River Watershed supplies area residents with potable water sourced from several reservoirs including Lake Hodges. Currently, about sixty-one percent (61%) of the WMA remains undeveloped or has been designated as open space. The remaining thirty-nine percent (39%) of the land area is being utilized as residential areas (18%), agriculture (14%), and other (7%). For further land use breakdowns by hydrologic area, please see the hydrologic area descriptions below.

The San Dieguito River Watershed is estimated to be home to approximately 178,000 residents (2010 U.S. Census). The vast majority of the population is concentrated in the more developed urban and suburban regions of the lower watershed, in the cities of Solana Beach and Del Mar, and the unincorporated community of Rancho Bernardo. Due in part to extensive development, the lower San Dieguito River bears a disproportionate share of the pollution burden when compared to portions of the watershed upstream. 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 San Dieguito River WMA extends through a diverse array of habitats from its eastern headwaters around the Cuyamaca Mountains to the outlet at the San Dieguito Lagoon and the Pacific Ocean. These areas help sustain a number of threatened and endangered species, including the Belding’s savannah sparrow, western snowy plover, and California least tern.

In fact, many of the water bodies support multiple beneficial uses, which include those listed in the table below.


~346 miles2

178,000 (2010 U.S. Census)
San Dieguito River, San Dieguito Lagoon, Lake Hodges, Sutherland Reservoir.
Coliform bacteria, nutrients, sediment, and trace metals.

  2010 Clean Water Act 303(d) List

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

Phosphorus, TDS
Aluminum, TDS
Chloride, Manganese, Pentachlorophenol (PCB), Sulfates
Pentachlorophenol (PCP), TDS
Color, Manganese, Mercury, Nitrogen, Phosphorus, Turbidity, pH
Enterococcus, Fecal Coliform, Nitrogen, Phosphorus, TDS, Toxicity
Color, Iron, Manganese, Total Nitrogen as N, pH

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


The San Dieguito 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  x
 Aquaculture (AQUA)  x
 Biological Habitats of Special Significance (BIOL)  x  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
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  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 San Dieguito River 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. The majority of pollutants impacting the San Dieguito WMA are attributed to urban runoff, agricultural runoff, and domestic animals.

Under Section 303(d) of the Clean Water Act, several water bodies within the San Dieguito River WMA were identified as impaired (see 303(d) table above). These impairments are 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 these water quality conditions.

Additionally, 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 the Regional Water Quality Control Board 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. The WQIP for the San Dieguito River WMA was submitted to and received approval from the Regional Water Quality Control Board in February 2016. Copermittees within the San Dieguito River WMA selected indicator bacteria in the San Dieguito River above and below Lake Hodges Reservoir as their highest priority water quality condition.



Solana Beach Hydrologic Area (905.1)

San Dieguito Lagoon

San Dieguito Lagoon (Credit, James Coffee)

Stretching from the Hodges Dam in the east to the Pacific Ocean in the west, the Solana Beach Hydrologic Area covers an area of about 31,000 acres. The most populated system within the WMA, it is also divided between the highest number of copermittees when compared to its counterparts. As such, jurisdiction over its municipal separate storm and sewer system is shared between the County of San Diego and the Cities of Solana Beach, Del Mar, and San Diego.

Where the San Dieguito River meets the Pacific Ocean lies San Dieguito Lagoon, a 150 acre estuary that recently underwent an extensive wetland restoration project aimed at improving water quality and reviving native species habitat. Similar to many of the wetland habitats in the San Diego region, the San Dieguito Lagoon provides refuge to a number of threatened and endangered bird species, including least terns and the Belding’s savannah Sparrow.

As a result of land disturbances in the area upstream, the lagoon has seen increased rates of sedimentation due to erosion. Currently, land use in the Solana Beach system is distributed accordingly: forty-four percent (44%) open space and undeveloped land, twenty-nine percent (29%) residential, eleven percent (11%) transportation, and ten percent (10%) agriculture. The remaining land area contains industrial, commercial, and other uses.

Partially due to heightened rates of sedimentation, there exists a delicate balance involved in maintaining water quality standards in San Dieguito Lagoon. When tidal flushing becomes restricted, pollutants have the tendency to collect in the Lagoon and can negatively impact water quality. As such, the Pacific Ocean near the mouth of the San Dieguito Lagoon has been listed as impaired for excessive concentrations of total coliform bacteria under Section 303(d) of the Clean Water Act. The San Dieguito River is also listed for fecal coliform bacteria, Enterococcus bacteria, nitrogen, phosphorus, total dissolved solids, and aquatic toxicity.

What marks the beginning of the Solana Beach Hydrologic Area in the east?

Hodges Hydrologic Area (905.2)

Lake Hodges

Lake Hodges –

Terminating at the Hodges Reservoir, the Hodges Hydrologic Area encompasses a land area of over 30,000 acres. Similar to the Solana Beach system, it is divided between several jurisdictions; namely, the County of San Diego and the Cities of Escondido, Poway, and San Diego.

The Hodges system includes a number of water bodies, such as Felicita Creek, Kit Carson Creek, and Lake Hodges Reservoir. Hodges Reservoir, which was expanded in 1918 to become the largest lake in the WMA, supplements other sources to supply water to residents and businesses in the San Diego region.

Land use in the Hodges Hydrologic Area mirrors that in Solana Beach, with open spaces and undeveloped lands constituting forty-four percent (44%) of the sub-watershed area. Residential areas are the second most common land use, accounting for thirty-six percent (36%) of the hydrologic area. Transportation is another significant land use, followed by several miscellaneous uses.

Several water bodies within the Hodges system have been listed as impaired under Section 303(d) of the Clean Water Act. This list includes Lake Hodges, which has been recognized as being affected by mercury, nitrogen, phosphorus, manganese, turbidity, and pH, among other pollutants. Felicita Creek is also considered impaired for total dissolved solids and aluminum.

In what year was the Hodges Reservoir expanded?

San Pasqual Hydrologic Area (905.3)

The San Pasqual Hydrologic Area is approximately 43,400 acres in size and makes up roughly twenty percent (20%) of the San Dieguito River WMA. The drainage basin lies within the jurisdictions of the Cities of Escondido, Poway, and San Diego, as well as the County of San Diego.

Land area of the San Pasqual Hydrologic Area is divided amongst open spaces and undeveloped lands (64%), agriculture (26%), residential (8%), and other land uses.

The majority of surface runoff to the region enters the Santa Ysabel Creek. However, there are also a number of smaller tributaries that feed into the creek, including Guejito Creek, Rockwood Canyon Creek, and Cloverdale Creek in San Pasqual Valley. One of these water bodies, Cloverdale Creek, has been listed as impaired under Section 303(d) of the Clean Water Act for total dissolved solids and phosphorus levels.

What is the primary water body within the San Pasqual Hydrologic Area?

Santa Maria Valley Hydrologic Area (905.4)

At roughly 37,000 acres, the Santa Maria Valley Hydrologic Area constitutes about seventeen percent (17%) of the San Dieguito River WMA. As the sole jurisdiction in the sub-watershed, monitoring and inspections of the area municipal separate storm and sewer systems falls entirely to the County of San Diego.

Primary water bodies within the system include Santa Maria Creek and Hatfield Creek. Most surface runoff is directed into one of these creeks and later enters the San Pasqual Hydrologic Area downstream.

The Cleveland National Forest, a 460,000 acre National Forest is located partially within the boundaries of the hydrologic area and contains a number of sensitive plant and animal species. Also located within the system is the Ramona Grasslands Preserve.

Here, open space and undeveloped lands constitute forty-one percent (41%) of its land area, followed closely by residential lands at thirty-five percent (35%) and agricultural lands at eighteen percent (18%).

What National Forest is located partially within the Santa Maria Hydrologic Area?

Santa Ysabel Hydrologic Area (905.5)

Santa Ysabel Creek (Above Sutherland Lake)

Santa Ysabel Creek (Above Sutherland Lake) – (Credit, James Coffee)

Far exceeding its counterparts in land area, the Santa Ysabel Hydrologic Area is approximately 82,000 acres in size. Although the County of San Diego has been named the sole copermittee for the system, the area also contains a considerable share of federal and state owned land and is home to a number of Indian Reservations. These lands are not subjected to the same requirements that local governments must adhere to, and therefore lie outside of the jurisdiction of the County of San Diego.

As the easternmost hydrologic area within the San Dieguito WMA, the system begins in the Volcan Mountains at the headwaters of Santa Ysabel Creek. Surface water is subsequently directed westward and is captured and consolidated behind the Sutherland Dam. Here, the Sutherland Reservoir isolates waters of the Santa Ysabel Hydrologic Area from water bodies situated in other hydrologic areas downstream, effectively cutting it off from the remainder of the WMA.

An immense range of endangered plant and animal species have been discovered in the Santa Ysabel Hydrologic Area. Twenty-two (22) were observed in the Cleveland National Forest, a 460,000 acre National Forest that lies partially within the Santa Ysabel system.

Lacking significant urbanization, open spaces and undeveloped land comprise roughly eighty-three percent (83%) of the Santa Ysabel Hydrologic Area. Remaining land in the system is dedicated to other uses, including agricultural (12%) and residential (4%) land uses.

Despite its lack of development, several water features within the Santa Ysabel system suffer from impairments. Santa Ysabel Creek, for example, is listed as impaired as a result of aquatic toxicity under Section 303(d) of the Clean Water Act. Also on the list is Sutherland Reservoir, which is impacted by a low pH and unexpectedly high concentrations of nitrogen, manganese, and iron.

Which dam is located within the Santa Ysabel Hydrologic Area?


“About the Forest.” Cleveland National Forest. USDA – Forest Service, n.d. Web. <>.

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

“San Diego County MS4 Copermittees. 2008. San Dieguito Watershed Urban Runoff Management Program. Final, March 2008. Submitted to the San Diego Regional Water Quality Control Board by the San Dieguito Copermittees.

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

San Dieguito Lagoon Interpretive Walk. Rep. San Dieguito River Park, 27 Dec. 2012. Web. <>.

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.