Santa Margarita Topography

The Carlsbad Watershed Management Area (WMA) is comprised of six (6) distinct hydrologic areas covering a land area of 211 square miles. The WMA extends from the headwaters above Lake Wohlford in the east to the Pacific Ocean in the west, and borders San Luis Rey and San Dieguito Watersheds to the north and south, respectively
There are numerous important surface hydrologic features within the Carlsbad WMA including four unique coastal lagoons, three major creeks, and two large water storage reservoirs. Unlike many of its neighboring WMAs, the Carlsbad WMA is also unique in that it is primarily comprised of independent and fully functional watersheds.

These include the following hydrologic areas:

  • Loma Alta (904.1)
  • Buena Vista Creek (904.2)
  • Agua Hedionda (904.3)
  • Canyon de las Encinas (904.4)
  • San Marcos (904.5)
  • Escondido Creek (904.6)

Currently, about thirty-two percent (32%) of the WMA remains undeveloped. The other major land uses making up the remaining sixty-eight percent (68%) of the land area are residential lands (29%), agricultural lands (12%), freeways and roads (12%), commercial and industrial lands (6%), and miscellaneous uses (9%). To see a more definitive breakdown of land uses by hydrologic area, please refer to the descriptions below.

One of the most densely populated portions of San Diego County, the Carlsbad WMA is estimated to be home to approximately 565,000 residents, based on 2010 U.S. Census data. Given its concentrated population, the watershed suffers from several pollutants, that have the potential to negatively impact how residents, business-owners, and tourists use and interact with local water bodies.

The WMA serves more than just humans, however. In fact, the Carlsbad WMA consists of a variety of unique and diverse ecosystems that act as critical habitat for a number of endangered species, including the California gnatcatcher, least bell’s vireo, and the orange-throated whiptail.

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


211 miles2

565,000 (2010 U.S. Census)
Loma Alta Creek, Buena Vista Creek, Buena Vista Lagoon, Agua Hedionda Creek, Agua Hedionda Lagoon, San Marcos Creek, Batiquitos Lagoon, Escondido Creek, San Elijo Lagoon, and Lake Wohlford.
Indicator bacteria, nutrients, and sediment.

  2010 Clean Water Act 303(d) List

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

Enterococcus, Fecal Coliform, Manganese, Phosphorus, Selenium, TDS, Total Nitrogen as N, Aquatic Toxicity
DDT, Nitrate, Nitrite
Sediment Toxicity, Selenium
Indicator Bacteria, Nutrients, Sedimentation/Siltation
DDT, Sediment Toxicity, Selenium
Selenium, Toxicity
DDT, Enterococcus, Fecal Coliform, Manganese, Phosphate, Selenium, Sulfates, TDS, Total Nitrogen as N, Toxicity
Selenium, Toxicity
Eutrophic, Indicator Bacteria
Indicator Bacteria, Total Coliform
Eutrophic, Indicator Bacteria, Sedimentation/Siltation
DDE, Phosphorus, Sediment Toxicity, Selenium
Ammonia as Nitrogen, Nutrients

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


The Carlsbad 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
 Estuarine Habitat (EST)  x
Hydropower Generation (POW)  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
Shellfish Harvesting (SHELL)  x
Spawning, Reproduction and/ or Early Development (SPWN)  x
Warm Freshwater Habitat (WARM)  x  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 the above beneficial uses and can result in actions such as beach closures and postings, etc. Agricultural and urban runoff, sewage spills, and livestock have been identified as primary contributing sources.

Under Section 303(d) of the Clean Water Act, multiple water bodies were listed as impaired for several different pollutants, as indicated in the 303(d) table above. These conditions 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)) under the region’s National Pollutant Discharge Elimination System (NPDES) Permit focus their treatment and cleanup efforts on these particular water quality conditions.

As part of the process, however, 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). A revised WQIP for the Carlsbad WMA was submitted to the Regional Water Quality Control Board for approval in June 2016.



Loma Alta Hydrologic Area (904.1)

The Loma Alta Hydrologic Area is situated at the northern end of the watershed management area (WMA). At just over 6,300 acres, the hydrologic area comprises only five percent (5%) of the Carlsbad WMA. The system is contained almost entirely within the City of Oceanside, but also lies partially within the jurisdictions of the City of Vista and the County of San Diego.

The majority of surface runoff here is directed into Loma Alta Creek and subsequently drains through Loma Alta Slough into the Pacific Ocean. A 107 acre wetland, the Slough is influenced by intermittent tidal forces and is known to provide valuable habitat to a variety of native plant and animal species.

The area is relatively urbanized, with open space and undeveloped land comprising just twenty-one percent (21%) of the land area. Significant portions of the Loma Alta Creek have been subject to human modifications; namely, the construction of concrete-lined channels. These alterations, among others, have contributed to the degradation and fragmentation of riparian habitat corridors and a reduction in the value of critical ecosystem services previously offered by the natural channel and wetlands.

Which jurisdiction contains the greatest share of the Loma Alta Hydrologic Area?

Buena Vista Creek Hydrologic Area (904.2)

Buena Vista Lagoon

Buena Vista Lagoon

The Buena Vista Creek Hydrologic Area encompasses a land area of roughly 14,400 acres and stretches inland approximately 10.6 miles. Located just south of the Loma Alta Hydrologic Area, it is divided among several different jurisdictions, including the City of Vista, the City of Oceanside, the City of Carlsbad, and the County of San Diego.

Many of the Carlsbad WMA hydrologic areas contain a number of common features and are quite comparable in layout; most notable is a primary creek or stream that deposits surface water into the Pacific Ocean by way of an estuary or lagoon. The Buena Vista Creek Hydrologic Area is no exception in this regard. The creek ends at Buena Vista Lagoon, where it eventually discharges into the ocean. Home to notable wildlife and many species of birds, the freshwater lagoon is separated from the ocean by a man-made weir. The lagoon also serves as a collecting point for fishermen and for local bird watchers.

The Buena Vista Creek Hydrologic Area’s open areas and ecological reserves provide refuge to wide arrays of native plants and animals, including a number of endangered and threatened species. In total, Buena Vista Creek and Buena Vista Lagoon Ecological Reserves sum to over 223 acres and are home to such flora as widgeon grass, pondweed, and arrow grass. They also provide valued habitat to terns, ducks, grebes, raccoons, and opossums, among countless other species.

Over eighty-seven percent (87%) of the watershed has been developed. The majority of that development is related to residential land uses, which comprise about fifty percent (50%) of the watershed land area. This is then followed by lands dedicated to transportation, commercially zoned land, and miscellaneous land uses.

Due in part to human activities associated with extensive development, Buena Vista Creek Lagoon was listed as impaired under Section 303(d) of the Clean Water Act for heightened bacterial levels and excessive concentrations of nutrients, sediments, and silt. Anthropogenic changes associated with construction, daily activities, and channelization of streams and creeks are also assumed to contribute to these water quality conditions.

Which ecological reserves can be found in the Buena Vista Creek Hydrologic Area?

Agua Hedionda Hydrologic Area (904.3)

Agua Hedionda Lagoon

Agua Hedionda Lagoon –

The Agua Hedionda Hydrologic Area is approximately 18,800 acres in size and makes up roughly fourteen percent (14%) of the Carlsbad WMA. Copermittees responsible for the Agua Hedionda Hydrologic Area include the Cities of Carlsbad, Vista, Oceanside, and San Marcos, as well as the County of San Diego.

The southwestern slopes of the San Marcos Mountains mark the beginnings of Agua Hedionda Creek, which subsequently flows a distance of just over 10 miles before discharging into the Pacific Ocean at Agua Hedionda Lagoon. The lagoon supports a number of beneficial uses including recreational activities and wetland habitat.

Between Carlsbad Highlands and Agua Hedionda Lagoon, the hydrologic area contains over 650 acres of Ecological Reserve land. Species supported by this land include California gnatcatchers, turkey vultures, and golden eagles. The diversity of habitats, ranging from coastal sage scrub to salt marsh and mudflat habitats, also supports a number of mammals, amphibians, and reptiles.

Over seventy percent (70%) of the system is developed (29% is open space or undeveloped), residential land uses lying at the forefront at thirty-three percent (33%). With continued development, habitat fragmentation and channel hydromodification have also accelerated.

Unfortunately, the Agua Hedionda Creek Hydrologic Area is not without impairments. The Creek itself has been listed as impaired under Section 303(d) of the Clean Water Act for heightened bacteria levels, toxicity, and elevated concentrations of manganese, phosphorus, selenium, nitrogen, and dissolved solids. The Agua Hedionda Lagoon, which had previously been listed as impaired, has seen significant improvements in overall water quality over the last few years that inevitably warranted removal from the 303(d) list of impaired water bodies.

What are the primary water quality issues facing Agua Hedionda Creek?

Canyon de las Encinas Hydrologic Area (904.4)

The smallest hydrologic area within the Carlsbad WMA, the Encinas system is only about 3,400 acres in size and is located entirely within the jurisdiction of the City of Carlsbad. A relatively minor creek, Encinas Creek, is the primary water body within the hydrologic area and flows directly into the Pacific Ocean. Industrial land uses constitute a significant portion of the land area here, which has ultimately resulted in the channelization of many of the smaller tributaries and creeks.

How does the Canyon de las Encinas Watershed compare to its counterparts in size?

San Marcos Hydrologic Area (904.5)

Batiquitos Lagoon

Batiquitos Lagoon –

At about 36,000 acres in area and comprising roughly twenty-eight percent (28%) of the WMA, the San Marcos Hydrologic Area is the second largest of the Carlsbad systems. One of its distinguishing features is that the Upper and Lower San Marcos Hydrologic Areas areas have been made largely independent of one another by the Lake San Marcos impoundment. As such an expansive system, monitoring of the San Marcos Hydrologic Area storm water conveyance system falls on the County of San Diego and the Cities of San Marcos, Escondido, Carlsbad, Vista, and Encinitas.

San Marcos Creek and Encinitas Creek are the two major tributaries in the hydrologic area, converging prior to discharging into the Pacific Ocean at Batiquitos Lagoon. Batiquitos Lagoon is located in the City of Carlsbad and encompasses 540 acres of wetland habitat, including least tern nesting sites. Without significant impairments of any beneficial uses, the lagoon serves as a prime example for many other water bodies in the region.

Approximately seventy-two percent (72%) of the watershed is developed (28% is open space or undeveloped), the leading land use being residential at thirty-three percent (33%). The Upper San Marcos Creek area supports agricultural (primarily in the County of San Diego), urbanized and open space land uses. Lower San Marcos, on the other hand, has a significant amount of open space and urbanized areas.

Similar to other portions of the Carlsbad WMA, channelization of sections of the tributaries to upper San Marcos Creek was utilized as a strategy to protect properties from flood damage. This channelization has had several negative impacts on the surrounding environment, including degradation and fragmentation of riparian habitat corridors and a reduction in the value of critical ecosystem services previously offered by the natural channel and wetlands. Furthermore, San Marcos Lake was identified under Section 303(d) of the Clean Water Act as impaired due to high concentrations of nitrogen and nutrients.

What separates the Upper and Lower San Marcos Hydrologic Area?

Escondido Creek Hydrologic Area (904.6)

As the most expansive and complex system in the Carlsbad WMA, the Escondido Creek Hydrologic Area covers a land area of roughly 54,100 acres and constitutes forty percent (40%) of the entire WMA. Extending approximately twenty-five (25) miles inland, it is also the southernmost hydrologic area in the WMA and borders San Dieguito Watershed to the South. The Escondido Creek Hydrologic Area is dominated primarily by unincorporated areas of the County of San Diego. The remaining land area is divided up between the Cities of Carlsbad, Escondido, Encinitas, San Marcos, and Solana Beach.

The hydrologic area contains the largest share of open space and undeveloped lands of any of its counterparts, only sixty percent (60%) being developed. As the second most common land use type, residential areas comprise thirty-four percent (34%) of the system.

The Escondido Creek Hydrologic Area meets the Pacific Ocean at San Elijo Lagoon, a wetland habitat of 576 acres. Prior to discharging into San Elijo Lagoon, however, the creek originates in Bear Valley in north central San Diego County, nearby Daley Ranch, a 3,000 acre conservation area managed by the City of Escondido. The watershed is also home to two reservoirs: Lake Wohlford and Dixon Lake. As a flood control measure, parts of Escondido Creek, specifically the portion draining through the City of Escondido, have been subject to concrete-lining and channelization.

The Escondido Creek system consists of a number of water bodies that are listed as impaired under Section 303(d) of the Clean Water Act. The San Elijo Lagoon is impacted primarily by indicator bacteria, eutrophic conditions, and sedimentation/siltation. Escondido Creek is listed for DDT, Enterococcus, Fecal Coliform, Manganese, Phosphate, Selenium, Sulfates, Dissolved Solids, Nitrogen, and Toxicity.

Which two reservoirs are located within the Escondido Hydrologic Area?


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

San Diego County MS4 Copermittees. 2016. Carlsbad Watershed Management Area Water Quality Improvement Plan (WQIP). Second revised draft, June 2016. Submitted to the San Diego Regional Water Quality Control Board by the Carlsbad WQIP Copermittees. Prepared by Moe Enterprises, LLC for the San Diego County MS4 Copermittees: City of Carlsbad, City of Encinitas, City of Escondido, City of Oceanside, City of San Marcos, City of Solana Beach, City of Vista, 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:

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.