The San Juan Hydrologic Unit (SJHU) encompasses a land area of 496 square miles within the borders of Orange, San Diego, and Riverside Counties, with approximately 70 percent of the area located in Orange County and 30 percent in San Diego County. The South Orange County (South OC) Watershed Management Area (WMA), also referred to as the San Juan WMA, includes the area that encompasses the SJHU as defined in the Water Quality Control Plan of the San Diego Basin. The South OC WMA is located in the northwestern corner of the San Diego Regional Water Quality Control Board's (RWQCB) jurisdiction.

The SJHU is divided into five distinct hydrological areas (HA) listed below:

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

Four of these HAs are within the South OC WMA (901.1 - 901.4) and two are within the jurisdiction of San Diego County (901.4 - 901.5). Additionally, the Permit allows the larger hydrologic unit to be separated into sub-watersheds to focus water quality prioritization and jurisdictional runoff management program implementation efforts. The SJHU is comprised of six subwatersheds, listed below:

  • Laguna Coastal Streams Watershed
  • Aliso Creek Watershed
  • Dana Point Coastal Streams Watershed
  • San Juan Creek Watershed
  • San Clemente Coastal Streams Watershed
  • San Mateo Creek Watershed

The cities shown in the image above, in addition to unincorporated Orange County and Orange County Flood Control District, (collectively the Copermittees) are responsible for operating an interconnected storm drain system in the South OC WMA which discharges stormwater and urban runoff pursuant to the National Pollutant Discharge Elimination Systems (NPDES) Municipal Separate Storm Sewer Systems (MS4) Permit. RWQCB administers the MS4 Permit for the San Diego Region.

South OC climate is typically dry from May through October and rainy from late October through April. In the SJHU, the South OC WMA has a population of about 550,000, and San Diego County has a population of about 25,000. 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 water quality concerns when compared to other SJHU areas. The South OC WMA is working to address these concerns, which have the potential to impact how residents, business owners, and tourists use and interact with local water bodies. Many of the water bodies support multiple beneficial uses, including those outlined in the table below.


496 square miles (70% Orange County, 30% San Diego County)

550,000 in Orange County (2018 Geomatics)
25,000 in San Diego County (2010 US Census)

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 Waters  Coastal Waters  Reservoirs and Lakes Ground Water
 Agricultural Supply (AGR)  x  x
 Aquaculture (AQUA)  x
 Biological Habitats of Special Significance (BIOL)  x  x
 Cold Freshwater Habitat (COLD)  x
 Commercial and Sport Fishing (COMM)  x
 Contact Water Recreation (REC-1)  x  x
Industrial Process Supply (PROC)
Industrial Service Supply (IND)  x  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  x
Warm Freshwater Habitat (WARM)  x
Wildlife Habitat (WILD)  x  x
*Beneficial water uses within the San Juan Hydrologic Unit 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.

To address these pollutants, 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 MS4 Permit (Order No. R9-2013-0001, as amended by Order Nos. R9-2015-0001 and R9-2015-0100) and focus on improving the quality of stormwater and non-stormwater discharges by Copermittees’ MS4s. Lacking outfalls in the SJHU, the County of San Diego has allowed Orange County Copermittees to lead WQIP efforts for the SJHU.

On June 20, 2018, the RWQCB accepted South OC WMA's proposed WQIP for the SJHU. South OC WMA Copermittees have chosen to focus treatment on the following three high priority water quality conditions:

  • Pathogens at beaches
  • Unnatural water balance/flow regime in stream reaches and coastal estuaries
  • Channel erosion/geomorphologic impacts and erosion in stream reaches

Based on the proposed long-term strategic vision, short-term strategies, optional strategies and clear milestones to trigger these strategies, it is reasonable to expect that this WQIP will result in significant improvement of beneficial uses in receiving waters.

For more information, please visit the Data Clearinghouse for the South OC WMA MS4 Copermittees at



Laguna Hydrologic Area (901.1)

Salt Creek Beach

The Laguna Hydrologic Area is entirely within the boundaries of Orange County. It encompasses 39,894 acres and is divided into three subwatersheds: Laguna Coastal Streams; Aliso Creek; and Dana Point Coastal Streams. The Laguna Coastal Streams Watershed includes portions of Aliso Viejo, Laguna Beach, and Laguna Woods and consists of the Laguna Canyon Creek watershed, which runs directly down the middle of this watershed and discharges into the Pacific Ocean in Laguna Beach, and several other smaller watersheds.

The Aliso Creek Watershed includes portions of Aliso Viejo, Dana Point, Laguna Beach, Laguna Hills, Laguna Niguel, Laguna Woods, Lake Forest, and Mission Viejo. Its main water body is Aliso Creek, a long, narrow coastal canyon which has headwaters in the Cleveland National Forest and discharges into the Pacific Ocean at Aliso Beach.

The Dana Point Coastal Streams Watershed includes portions of Laguna Beach, Laguna Niguel, and Dana Point. Its main tributary is Salt Creek, which ultimately drains into the Pacific Ocean near the northern boundary of the City of Dana Point. The Dana Point Harbor is also located within this watershed.

Mission Viejo Hydrologic Area (901.2)

San Juan Creek River Outlet

The Mission Viejo Hydrologic Area is entirely within the boundaries of Orange County. It encompasses 101,279 acres and represents the San Juan Creek Watershed. The largest of the region's watersheds, the San Juan Creek Watershed includes portions of Dana Point, Laguna Hills, Laguna Niguel, Mission Viejo, Rancho Santa Margarita, and San Juan Capistrano. Its main tributary, San Juan Creek, originates in the Santa Ana Mountains district of the Cleveland National Forest.

San Clemente Hydrologic Area (901.3)

Sunset over West Reef at San Clemente Pier

The San Clemente Hydrologic Area is located in the southernmost part of Orange County. It encompasses 12,597 acres and represents the San Clemente Coastal Streams Watershed. The San Clemente Coastal Streams Watershed includes portions of San Clemente, San Juan Capistano, and Dana Point. Prima Deshecha Canada is one of two main streams that flow through the City of San Clemente, ultimately discharging into the Pacific Ocean at Poche Beach. The second main stream draining the watershed is Seguna Deshecha Canada, which discharges into the Pacific Ocean at North Beach.

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.

  • Adopt A Channel! OC Public Works's Adopt A Channel Program allows individuals, organizations, and businesses to adopt a portion of an Orange County flood control channel in order to carry out periodic trash cleanups. In doing so, Adopters positively impact our waterways, set examples and raise awareness of the effects of keeping our waterways clean and healthy, and are recognized for their commitment to community stewardship. Become an Adopter today!

  • Think about replacing sod and other water-intensive shrubbery with drought-tolerant landscaping. As a result of drought, many jurisdictions and water agencies offer rebates and other incentives to remove natural turf and install rain barrels and other water capture devices. This will save you money and 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 from getting into our waterways.

  • Volunteer for a clean up event. 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 into creeks, rivers, and ocean waters during rain events. Consider carrying a bag with you to collect litter as you take your morning or evening stroll.

  • Implementation and adaptation of the WQIP is an ongoing process and 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 website for upcoming meetings.

  • Report Pollution. If you observe any discharges of water that you believe may be illicit, then do not hesitate to report it by means of our contacts page.

  • ...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 family, friends, and coworkers.