Santa Margarita Topography

The Santa Margarita Watershed encompasses a land area of roughly 750 square miles, of which about 200 square miles, or twenty-seven percent (27%), lies within San Diego County. The watershed is located in northern San Diego and southwestern Riverside Counties and borders San Juan Watershed to the northwest and San Luis Rey Watershed to the south.

The Santa Margarita Watershed can be divided into nine distinct hydrological areas, each with unique hydrological and environmental features:

  • Ysidora (902.1)
  • De Luz (902.2)
  • Murrieta (902.3)
  • Auld (902.4)
  • Pechanga (902.5)
  • Wilson (902.6)
  • Cave Rocks (902.7)
  • Aguanga (902.8)
  • Oakgrove (902.9)

Of these nine hydrologic areas, only 5 are located at least partially within the jurisdiction of the County of San Diego:

  • Ysidora (902.1)
  • De Luz (902.2)
  • Pechanga (902.5)
  • Aguanga (902.8)
  • Oakgrove (902.9)

For the purposes of this overview, these portions of the watershed within the County of San Diego will be referred to here as the Santa Margarita WMA. Rainfall to the area primarily drains through the Santa Margarita River, which originates where the Temecula and Murrieta Creek systems meet near the City of Temecula, in Riverside County. The river eventually discharges to the Pacific Ocean after flowing through several unincorporated areas, the community of Fallbrook, and the Marine Corps Base Camp Pendleton.

Of the Santa Margarita WMA, undeveloped and open spaces constitute approximately forty-four percent (44%) of the land area, followed by military uses at thirty percent (30%), residential at eight percent (8%), agriculture at seven percent (7%) and miscellaneous land uses at eleven percent (11%). To see a more detailed breakdown by hydrologic area, please see specific hydrologic area sections below.

According to 2010 U.S. Census data, the Santa Margarita Watershed is estimated to be home to approximately 320,000 residents, of which about 28,000 are located in San Diego County. Currently, the majority of development is concentrated in Riverside County, in the upper watershed basin. Without effective planning measures in place, however, a major concern is that this spur in development could exacerbate current surface water quality problems downstream.

The lower river and estuary have largely escaped the development typical of other regions of coastal Southern California, and are therefore able to support a relative abundance of functional habitats and wildlife. In fact, Santa Margarita Watershed is home to some of the largest populations of endangered and threatened species in Southern California. Its swaths of predominately untouched land act as critical habitat to approximately seventy (70) Federally- and State-listed endangered and threatened species, including the arroyo toad, the pacific pocket mouse, the southwestern willow flycatcher, and the least bell’s vireo. Offshore, moreover, it is not a rarity to observe a number of marine animals of special concern.

These include species like Guadalupe fur seals, the Pacific loggerhead turtle, and the blue whale, among others. Like other watersheds, the bodies of water within the Santa Margarita Watershed have been assigned beneficial uses.


200 miles2 in SD County and ~750 miles2total.

28,000 in SD County and ~320,000 total.1
Santa Margarita River, Temecula Creek, Murrieta Creek, Santa Margarita Lagoon, Vail Lake, Skinner Reservoir, and Diamond Valley Lake Reservoir.

Nitrate (surface and groundwater), sediment, indicator bacteria, and total dissolved solids in groundwater.

  2010 Clean Water Act 303(d) List

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

Iron, Manganese, Nitrogen, Sulfates
Chlorpyrifos, Fecal Coliform, Iron, Manganese

Enterococcus, Fecal Coliform, Phosphorus, Total Nitrogen as N

Chlorpyrifos, Copper, Iron, Manganese, Nitrogen, Phosphorus, Toxicity

Iron, Nitrogen, Phosphorus, Sulfates, TDS

Chlorpyrifos, Copper, Diazinon, E. Coli, Fecal Coliform, Iron, Manganese, Nitrogen, Phosphorus, TDS

Iron, Sulfates, TDS

Chlorpyrifos, Copper, E. coli, Fecal Coliform, Iron, Manganese, Phosphorus

Chlorpyrifos, Copper, Phosphorus, TDS, Toxicity

Phosphorus, Toxicity

Chlopyrifos, E. coli, Fecal Coliform, Iron, Manganese, Phosphorus, Total Nitrogen as N

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


The Santa Margarita WMA contains a number of environmentally sensitive areas (ESAs), as defined in Chapter 5 of the San Diego Regional Basin Plan.

Learn More


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  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
*Beneficial water uses within the Santa Margarita Watershed as designated in the State Water Resources Control Board’s San Diego Region Basin Plan


Under Section 303(d) of the Clean Water Act, a number of water bodies from the Santa Margarita WMA were determined to be impaired due to excessive nutrients, an issue that is required to be addressed through a number of best management practices in conjunction with regular monitoring. As such, Copermittees (also referred to as Responsible Agencies (RAs)) focus their treatment and cleanup efforts on this particular water quality condition. Because the Santa Margarita Watershed crosses county borders, these efforts require a significant amount of collaboration from agencies in both San Diego and Riverside Counties.

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, newly listed threatened and endangered species, etc. Several sources have been identified as impacting the above beneficial uses, including: agricultural areas, orchards, livestock, domestic animals, septic systems, use of recycled water, and urban runoff.

As part of the process, 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). The Santa Margarita WMA WQIP has been submitted to the Regional Water Quality Control Board for approval.



Ysidora Hydrologic Area (902.1)

Situated near the border of San Diego County, the Ysidora Hydrologic Area covers a land area of about 28,000 acres. The County of San Diego manages all outfalls associated with the storm water conveyance system for the portion of the Santa Margarita Watershed that lies within its borders (hereby referred to as the Santa Margarita WMA), including the entirety of the Ysidora Hydrologic Area.

Overlapping significantly with Marine Corps Base Camp Pendleton, the Santa Margarita River Estuary delineates the point at which the Santa Margarita River meets the Pacific Ocean. The Estuary is home to a variety of mammalian, fish, plant, and bird species, including the tidewater goby, the California least tern, and the western snowy plover.

The region is protected from most urban and suburban development due to its military land use; however, water quality conditions further upstream still exert significant pressures on the Ysidora system. Accordingly, land within the sub-watershed is predominately military lands (89%), other land uses being residential (4%) and agricultural (2%).

Despite ongoing efforts by the County of San Diego and Riverside County copermittees, the Ysidora Hydrologic Area contains several water bodies that have been listed as impaired under Section 303(d) of the Clean Water Act. These include the Santa Margarita River Lagoon, which is considered eutrophic, and the lower Santa Margarita River, listed as impaired for enterococcus, coliform bacteria, phosphorus, and nitrogen.

Which Marine Corps Base is located in the Ysidora Hydrologic Area?

De Luz Hydrologic Area (902.2)

Santa Margarita Ecological Reserve

Santa Margarita Ecological Reserve –

The largest Santa Margarita system within the jurisdiction of San Diego County, the De Luz Hydrologic Area covers a land area of nearly 41,000 acres. As there are no overlapping municipalities here, the County is the only jurisdiction within this portion of the De Luz Hydrologic Area.

Undeveloped lands and open spaces make up the largest share of the De Luz Hydrologic Area, at forty-two percent (42%). In addition, Marine Corps Base Camp Pendleton comprises about thirty-one percent (31%) of the system’s area, followed by residential lands at fourteen percent (14%) and agriculture at twelve percent (12%). The system also contains a small fraction of the 4,340 acre Santa Margarita Ecological Reserve, home to thirty (30) miles of protected riparian habitats alongside Santa Margarita River.

A number of water features located here have been singled out as impaired under Section 303(d) of the Clean Water Act. For example, the upper reaches of the Santa Margarita River have been noted as impacted by phosphorus and aquatic toxicity. Similarly, Rainbow Creek was listed for nitrogen, phosphorus, iron and sulfates.

Santa Margarita Ecological Reserve encompasses how many miles of protected riparian corridor?

Pechanga Hydrologic Area (902.5)

Riverside County copermittees are held responsible for most of the municipal separate storm sewer systems (MS4s) in the Pechanga Hydrologic Area, although the County of San Diego manages the storm water conveyance system in the 1,280 acres within its jurisdiction.

With undeveloped and open space lands constituting ninety-nine percent (99%) of the land area, the Pechanga Hydrologic Area remains largely in its natural state. Because such a small portion of the Pechanga system is within San Diego County, most impaired water bodies are monitored by Riverside County copermittees.

The majority of the Pechanga Hydrologic Area lies within which county?

Aguanga Hydrologic Area (902.8)

Located near the upper reaches of the Santa Margarita WMA, the Aguanga Hydrologic Area encompasses approximately 20,000 acres and about sixteen percent (16%) of the area within San Diego County’s jurisdiction. No additional municipalities are contained within this portion of the sub-watershed, so the County of San Diego is the only permittee in this area.

Land usage in the Aguanga Hydrologic Area parallels that in the Pechanga Hydrologic Area. The system is almost completely untouched, with undeveloped lands and open spaces constituting ninety-nine percent (99%) of the land area.

Which is the sole jurisdiction within the Aguanga Hydrologic Area?

Oakgrove Hydrologic Area (902.9)

The Oakgrove Hydrologic Area encompasses about 36,000 acres of land in the headwaters of the Santa Margarita WMA. As is the case with its counterpart hydrologic areas, the County of San Diego is the only jurisdiction here. It remains mostly undeveloped, agricultural and residential land areas constituting only about seven percent (7%) each of the system.

Where is the Oakgrove Hydrologic Area located relative to the rest of the Santa Margarita WMA?


Integrated Natural Resources Management Plan. Rep. N.p.: Marine Corps Base Camp Pendleton, n.d. Marines. Marine Corps Base Camp Pendleton, Mar. 2012. Web. <[1].pdf>.

San Diego County MS4 Copermittees. 2008. Santa Margarita River Watershed Urban Runoff Management Program (WURMP). Final, March 24, 2008. Submitted to the San Diego Regional Water Quality Control Board by the 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.

Upper Santa Margarita Watershed Integrated Regional Water Management Plan Update. Final, April 2014. Submitted to the San Diego Regional Water Quality Control Board by the County of Riverside, the Rancho California Water District, the Riverside County Flood Control and Water Conservation District, and the Stakeholder Advisory Committee.


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.