San Juan WMA 2017-02-02T18:26:49+00:00


Santa Margarita Topography

The San Juan Watershed encompasses a land area of 496 square miles, of which about 150 (30%) are within the borders of San Diego County. For the purposes of this summary, the portion in the County of San Diego will be referred to as the San Juan Watershed Management Area. The WMA lies in the northern portion of the County and neighbors Orange and Riverside to the north and Santa Margarita Watershed to the south.

The watershed is divided into five distinct hydrological areas, each with unique geological and environmental features:

  • Laguna (901.1)
  • Mission Viejo (901.2)
  • San Clemente (901.3)
  • San Mateo Canyon (901.4)
  • San Onofre (901.5)

However, only two of these are at least partially within the jurisdiction of San Diego County: San Mateo Canyon and San Onofre. Rainfall to the area drains through a number of minor creeks and tributaries, all eventually discharging to the Pacific Ocean; although, it is not unusual for these creeks to be dry from July through November. The topography of the San Onofre and San Mateo Hydrologic Areas is varied, ranging from coastal plains in the western portion to the Santa Margarita Mountains, which rise over 2,000 feet above mean sea level.

Currently, the majority of the WMA lies within the confines of Marine Corps Base Camp Pendleton, although much of that land remains undeveloped.

The San Juan WMA is estimated to be home to approximately 25,000 people located in San Diego County. The vast majority of the population is concentrated in the more developed urban and suburban coastal regions of Orange County, which bears a disproportionate share of the pollution burden when compared to other portions of the watershed.

The San Juan 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.

Marine Corps Base Camp Pendleton, which lies in the San Diego County share of the watershed, is supplied with water primarily from groundwater sources, by way of local wells. It is important to note, however, that the watershed serves more than just humans. The San Juan WMA consists of a wide array of ecosystems that support eighteen (18) threatened or endangered plant and animal species.

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


496 miles2 (~150 of which are in San Diego County)

25,000 in San Diego County (2010 US Census)
Orange County, Aliso Creek, San Juan Creek, Dana Point Harbor

Coliform bacteria, nutrients, total dissolved solids, solvents, trace metals, and petroleum.

  2010 Clean Water Act 303(d) List

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

Indicator Bacteria, Phosphorus, Selenium, Toxicity, Total Nitrogen as N
Diazinon, Phosphorus, Total Nitrogen as N, Toxicity
Copper, Toxicity, Zinc
Benzo(b)fluoranthene, Dieldrin, Sediment toxicity, Selenium
Sediment toxicity, Toxicity
Total Coliform, Enterococcus, Fecal Coliform, Indicator Bacteria
Selenium, Toxicity
Chloride, Sulfates, Total Dissolved Solids, Selenium, Toxicity
Cadmium, Nickel, Phosphorus, Turbidity
DDE, Indicator Bacteria, Phosphorus, Selenium, Total Nitrogen as N, Toxicity
Phosphorus, Toxicity, Turbidity

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


The San Juan 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 LakesGround Water
 Agricultural Supply (AGR) x x
 Aquaculture (AQUA) x
 Biological Habitats of Special Significance (BIOL) x
 Cold Freshwater Habitat (COLD) x
 Commercial and Sport Fishing (COMM) x
 Contact Water Recreation (REC-1) x x
Industrial Service Supply (PROC) x x
Marine Habitat (MAR) x
Migration of Aquatic Organisms (MIGR) x
Municipal and Domestic Supply (MUN) x
Navigation (NAV) x
Non-Contact Water Recreation (REC-2) 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
Wildlife Habitat (WILD) x
*Beneficial water uses within the San Juan 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 San Juan WMA (San Diego County), these pollutants are primarily assumed to originate from urban and agricultural runoff as well as military operations.

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). Lacking outfalls in the San Juan WMA, the County of San Diego has allowed Orange County copermittees to lead WQIP efforts.

The WQIP for the WMA is still in development and upon completion, will be submitted to the Regional Water Quality Control Board for approval. Orange County copermittees have chosen to focus treatment on pathogens at area beaches and geomorphological impacts and erosion within the streams, conditions which have been classified as highest priority water quality conditions.



San Mateo Canyon Hydrologic Area (901.4)

The San Mateo Canyon Hydrologic Area is divided up amongst the Counties of Riverside, Orange, and San Diego. Headwaters for the system are located in Riverside County; however, it drains runoff from all three counties before discharging to the Pacific Ocean in San Diego County. Approximately 31,000 acres of the system lies within the borders of San Diego County.

Of the portion that is within San Diego County, approximately fifty-three percent (53%) is incorporated into Marine Corps Base Camp Pendleton. The remaining portions are unincorporated and include some park lands and other open spaces.

The primary water body within the system of course, is San Mateo Creek. It is fed by a number of smaller creeks and tributaries, including Christianitos Creek. Water bodies within the San Mateo Hydrologic Area have fortunately avoided many of the water quality issues that are present in many developed watersheds, and as such, have avoided any 303(d) listings.

Which Marine Corps Base is located in the San Mateo Canyon Hydrologic Area?

San Onofre Hydrologic Area (901.5)

The San Onofre Hydrologic Area is completely within the boundaries of the County of San Diego. It encompasses approximately 37,500 acres near the northern border of the County and is dedicated primarily to military uses associated with Marine Corps Base Camp Pendleton. In fact, only about three percent (3%) of the land within the hydrologic area is not military land.

The system contains a number of important water features, including San Onofre and Jardine Creeks. These creeks, along with their associated tributaries, converge in San Onofre Valley before discharging into the Pacific Ocean. Similar to the San Mateo Canyon Hydrologic Area, the San Onofre Hydrologic Area has largely avoided the impairments that plague more developed watersheds.

What portion of the San Onofre Hydrologic Area is dedicated to military uses?


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

South Orange County MS4 Copermittees. 2016. South Orange County (San Juan Hydrologic Unit) Water Quality Improvement Plan (WQIP). Draft, April 1, 2016. Submitted to the San Diego Regional Water Quality Control Board by the San Juan Copermittees.

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.