Santa Margarita Topography

The San Luis Rey Watershed encompasses a land area of about 560 square miles. It lies in the northern portion of the County and neighbors Santa Margarita Watershed to the north and Carlsbad and San Dieguito Watersheds to the south.

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

  • Lower San Luis Rey (903.1)
  • Monserate (903.2)
  • Warner Valley (903.3)

Rainfall to the area primarily drains through the San Luis Rey River, which stretches east to west over a length of about fifty-five (55) miles and originates in the Palomar and Hot Springs Mountains. The river eventually discharges to the Pacific Ocean near the City of Oceanside.

San Luis Rey Watershed supplies area residents with potable water sourced from Turner Reservoir and Lake Henshaw, as well as a number of underground aquifers. Lake Henshaw drains approximately 209 square miles of land located in the Warner Valley Hydrologic Area, in the eastern third of the watershed. The WMA also is home to six groundwater aquifers: Warner, Pauma, Pala, Bonsall, Moosa, and Mission Basins.

Currently, about fifty-four percent (54%) of the watershed management area (WMA) remains undeveloped. The remaining forty-six percent (46%) of the land area is being utilized for residential areas (15%), agricultural uses (14%), and other uses. Roughly fourteen percent (14%) of the watershed is also comprised of six (6) federally recognized Tribal Indian Reservations. For more detailed breakdowns by hydrologic area, please see the Lower San Luis Rey, Monserate, and Warner Valley Hydrologic Area descriptions below.

The San Luis Rey Watershed is estimated to be home to approximately 166,000 residents, according to 2010 US Census data. The population is most highly concentrated downstream in and around the Cities of Oceanside and Vista. Particularly near these more urbanized areas, water bodies suffer from several pollutants, which have the potential to negatively impact how residents, business-owners, and tourists use and interact with them.

It is important to note that the watershed serves more than just humans. The San Luis Rey Watershed consists of a variety of unique and diverse ecosystems that act as critical habitat for several species of concern, including the orange-throated whiptail, western skink, and the California pocket mouse.

Water bodies here support multiple beneficial uses, including those listed in the table below.


560 miles2

166,000 (2010 U.S. Census)

San Luis Rey River, Lake Henshaw.

Indicator bacteria and nutrients.

  2010 Clean Water Act 303(d) List

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


Chloride, Enterococcus, Fecal Coliform, Phosphorus, TDS, Total Nitrogen as N, Toxicity

Enterococcus, Total Coliform

Total Nitrogen as N

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


The San Luis Rey 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  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
Freshwater Replenishment (FRSH) x  x  x
Industrial Process Supply (PRO)  x  x  x
Industrial Service Supply (PROC)  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 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.

Under Section 303(d) of the Clean Water Act, the Lower San Luis Rey Watershed was identified as impaired for a number of pollutants, including, but not limited to: selenium, Enterococcus bacteria, total coliform bacteria, chloride, phosphorus and total dissolved Solids. These conditions are expected to be addressed through a number of best management practices and regular monitoring. Major sources of pollutants in the San Luis Rey WMA include agriculture, orchards, livestock, domestic animals, urban runoff, and septic systems.

As part of the process, copermittees (also referred to as Responsible Agencies (RAs)) 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 Luis Rey WMA, copermittees include the County of San Diego and the Cities of Oceanside and Vista.

The final WQIP for the San Luis Rey 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 in the Lower San Luis Rey River, a condition which has been classified as highest priority water quality condition.



Lower San Luis Rey Hydrologic Area (903.1)

San Luis Rey River

San Luis Rey River –

Land area within the San Luis Rey WMA is fairly evenly distributed between its three hydrologic areas, each encompassing slightly over 100,000 acres. Nevertheless, despite this even land distribution, all incorporated areas of the watershed are located in the Lower San Luis Rey system. As such, monitoring and inspections of the hydrologic area’s municipal separate storm and sewer systems are performed by the County of San Diego and the Cities of Vista and Oceanside.

Water that drains through the basin eventually finds its way to the Pacific Ocean by way of the San Luis Rey River Estuary. The approximately 164 acres of wetland in the estuary are known to provide critical habitat to several species of concern, including the least bell’s vireo, southwestern pond turtle, and the belding’s savannah sparrow.

The most developed sub-watershed in the San Luis Rey WMA, its land area is divided up between residential (35%), agricultural (25%), and military (7%) land uses. Approximately twenty-one percent (21%) of the area remains undeveloped or is being maintained as open space and park lands.

Relative to its counterpart hydrologic areas, the San Luis Rey system suffers from the most pressing water quality issues. Under Section 303(d) of the Clean Water Act, for example, lower San Luis Rey River was listed as impaired for chloride, enterococcus, fecal coliform, phosphorus, total dissolved solids (TDS), total nitrogen as N, and toxicity.

How does the Lower San Luis Rey Hydrologic Area compare to the rest of the watershed in terms of development?

Monserate Hydrologic Area (903.2)

Wilderness Gardens Preserve

Wilderness Gardens Preserve –

The Monserate Hydrologic Area constitutes a land area of over 100,000 acres and makes up nearly one-third of the area of the San Luis Rey WMA. Unlike the San Luis Rey Hydrologic Area, however, area municipal separate storm and sewer systems are managed entirely by the County of San Diego.

Encompassing nearly 740 acres of the system, the Wilderness Gardens Preserve provides locals with a number of hiking trails and includes habitat for various species identified to be of concern either federally or at the state level. These include the orange-throated whiptail, western skink, California pocket mouse, San Diego pocket mouse, Mexican long-tongued bat.

Development in the San Luis Rey watershed has been focused more towards coastal areas of the WMA. Lying in between the Lower San Luis Rey and Warner Valley Hydrologic Areas, the Monserate Hydrologic Area has experienced an intermediate level of development. Here, undeveloped lands still constitute about seventy-two percent (72%) of land area, followed by agriculture at seventeen percent (17%) and residential at nine percent (9%).

Also located within the boundaries of the Monserate system are portions of the Pala, Pauma, La Jolla, Rincon, and Uima Indian Reservations. These lands are not subject to the requirements of the regional MS4 permit and are therefore not included within the scope of the San Luis Rey WQIP and its efforts.

Which reservations are located in the Monserate Hydrologic Area?

Warner Valley Hydrologic Area (903.3)

Making up the headwaters of the watershed, the Warner Valley Hydrologic Area covers a land area of about 133,000 acres and is managed entirely by the County of San Diego.

Located near the edge of the hydrologic area lies Lake Henshaw, a reservoir established with the construction of the Henshaw Dam in 1923. The entirety of the sub-watershed drains to the reservoir, which has a storage capacity of about 52,000 acre-feet and provides water to the northern portions of San Diego County.

Remaining largely untouched, about ninety-one percent (91%) of the Warner Valley system is made up of undeveloped and open space lands. The system also encompasses lands belonging to a number of federally recognized tribes; namely the Santa Ysabel and Los Coyotes Indian Reservations.

What year was the Henshaw Dam constructed?


“Reservoirs.” San Diego County Water Authority. San Diego County Water Authority, 24 Oct. 2016. Web. <>.

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

San Diego County MS4 Copermittees. 2016. San Luis Rey Watershed Management Area Water Quality Improvement Plan (WQIP). Final, March 2016. Submitted to the San Diego Regional Water Quality Control Board by the San Luis Rey Copermittees. Prepared by Larry Walker & Associates and Amec Foster Wheeler Environment & Infrastructure, Inc. for the San Diego County MS4 Copermittees: California Department of Transportation, City of Oceanside, City of Vista, County of San Diego.

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

“San Luis Rey River Estuary.” California Natural Resources Agency, 2007. 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 pet 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.