San Diego River Watershed

The San Diego River Watershed (SDRW) is the second largest watershed (440 square miles) in San Diego County and has the greatest population base (approximately 509,000 people). Water resources in the watershed include the San Diego River main stem, numerous tributaries, 22 steams, five water supply reservoirs (El Capitan, San Vicente, Lake Jennings, Lake Murray, and Cuyamaca Reservoirs), a large groundwater aquifer, extensive riparian habitat, coastal wetlands, and tidepools.

Lake Cuyamaca drainage area prior to 2003 fires  (San Diego River Watershed)                         Photo by Marcello Mastrocola*


Prior to 2003 fires                                                                                    photo from Cuyamaca Rancho State Park Website


Lake Cuyamaca drainage area after the 2003 fires  (San Diego River Watershed)                              Photo by Barbara Barnes

The size, complexity, and geographical variations of the SDRW suggests that the assessment of its resources can best be made by dividing the watershed into three major sub-basins, or management areas: The El Capitan Management Area; the San Vicente Management Area; and the San Diego Management Area. Each sub-basin is hydraulically disconnected.

The network of primary streams and reservoirs within the watershed are presented below by sub-basins.

Stream Network of the San Diego River Watershed


(Management Areas)

Stream/Water Body 
Cuyamaca Reservoir
San Diego River
Boulder Creek
El Capitan

Cedar Creek

Chocolate Creek
Ritchie Creek
Kelly Creek
Isham Creek
Sand Creek
Peutz Creek
San Vicente Reservoir
San Vicente Creek
Swartz Canyon Creek
Klondike Creek
San Vicente
Santa Ana Creek
Longs Gulch
West Branch San Vicente Creek
Padre Barona Creek
San Diego River Estuary
Forester Creek
Lower San Vicente Creek
Los Coches Creek
San Diego 

Wildcat Canyon Creek

Little Sycamore Canyon Creek
Oak Canyon Creek
Murphy Canyon Creek


Topographic elevations range from sea level at the mouth of the river at Ocean Beach to the eastern edge of the watershed near Julian at an elevation of  6,512 feet.  Elevation influences several important conditions that affect watershed management.  These include:

Precipitation. There is a strong, topographically-influenced orographic effect on precipitation in the SDRW. Higher elevations receive an average of more than 30 inches per year, whereas, lower coastal plains receive an average of less than 12 inches per year.

Slope stability. Areas with rougher topography (combined with greater precipitation levels) in the higher elevations of the watershed are more prone to problems related to slope stability, such as erosion. Soil characteristics in this area include erodibility.

Vegetation. Elevation plays an important role in the natural abundance of different plant species in the watershed. Vegetation can help prevent slope instability. Temperature, precipitation, and light levels vary with topography, and these factors affect the species diversity and abundance of the vegetation.

Approximately 58 percent of the SDRW is  undeveloped, primarily in the upper reaches; the highly urbanized area is found in the lower reaches. The undeveloped lands, including the Cleveland National Forest and Mission Trails Regional Park, host a wide variety of habitats and endangered species likethe Arroyo Toad, Least Bell’s Vireo, and the Southwestern Pond Turtle.

The San Diego River originates in the mountains northwest of the historic town of Julian and runs southwestward through an unincorporated, largely uninhabited area of San Diego County before entering El Capitan Reservoir. Downstream of El Capitan Reservoir, the river flows westward through the Cities of Santee and San Diego and past Famosa Slough to the San Diego River Estuary. Famosa Slough and the estuary are extremely productive wetland habitats. The river discharges into the Pacific Ocean just south of the jettied entrance of Mission Bay in the community of Ocean Beach. Primary tributaries to the San Diego River include Boulder Creek, Cedar Creek, Conejos Creek, Chocolate Creek, Los Coches Creek, San Vicente Creek, and Forester Creek, as shown below.

 Famosa Slough (Ocean Beach)                                Photo by Scott Streit*

Watershed Threats

Threats to the watershed resources found in the SDRW include: water quality degradation by toxic chemicals, bacteria, and total dissolved solids (TDS); excessive extraction of groundwater; proliferation of invasive species; runoff containing excessive levels of nutrients and sediments; flooding; aggregate mining operations; and habitat loss and modification. Many human activities generate these threats. Automobile use contributes to polluted runoff from roads and the deposition of metals and airborne pollutants.  Environmentally insensitive housing and commercial developments and farming techniques can compromise wetlands and increase sediment transport to the river and its reservoirs. Gravel mining alters the hydrology and contributes to TDS and turbidity issues in the watershed. Demands for water supply in the watershed bring large quantities of imported water that contains high levels of TDS. Groundwater extraction and damming of the river and its tributaries can have a profound influence on the quantity and quality of surface waters in the watershed.

The mouth of the river discharges into the Pacific Ocean at the community of Ocean Beach. Beach in Mission Bay Park postings and closures due to elevated levels of coliform bacteria more than doubled between 1996 and 1999 due to urban runoff and sewage spills. The extensive groundwater resources associated with the San Diego River provide a cost- effective and reliable water supply to four local water districts and the City of San Diego.  Excessive extraction, increasing TDS, and Methyl Tertiary Butyl Ether (MTBE) contamination now threaten this resource.

Generally speaking, the water quality in the upper watershed is of much higher quality than the lower watershed. The upper watershed’s water quality is high due to the undeveloped nature of that area. The lower watershed’s surface water quality is generally poor; this is due to over 50 years of development and hydromodifications that have adversely impacted surface water quality.


Post-fire Impacts on the El Capitan Management Area of the Watershed

Pre-fire source water and reservoir monitoring in the El Capitan Management Area showed the primary COC were turbidity, nutrients, bacterial indicators, and TDS.  The soils in this management area are primarily Cieneba and Fallbrook, both of which are found in rolling to mountainous uplands; these soils naturally havemoderate to very high erosion hazard ratings and rapid runoff, and are vulnerable to increased mud flows after a fire has removed vegetation. Therefore, effects of the Cedar Fire on El Capitan Reservoir include increased sedimentation with some loss of storage and turbidity during peak runoff events; storage appears to be adequate to handle the reduction.

The major post-fire pathways for the transport of various constituents are mudslides and erosion, which carry nutrients and increase turbidity. Temporary changes in water quality within this management area will very likely occur during watershed runoff events. In response, the SDWD will incur additional near-term water treatment costs due to post-fire inputs of sediment, ash, and nutrients. Long-term, the nutrients previously locked in the vegetation will continue to enter the reservoir as ash and sediment after storm events. Depending on the severity of the storms in the few years following the fire, the management area may be able to recover sufficiently to prevent nutrient loading to the reservoir. The SDWD may expect increased algae blooms and odor and taste concerns for at least five to ten years following the fire. SDWD is coordinating with the Natural Resources Conservation Service for financial assistance for addressing water treatment problems stemming from the burned area emergency.

                                        Boulder Creek (Pre-Cedar Fire, March 2003)                                                                      Photo by Jimmy Smith*                                                                                                

The El Capitan Management Area suffered the highest degree of soil burn severity in the entire SDRW. Immediate actions taken to control the sedimentation include: culvert cleaning and replacement, hydromulching, debris and hazardous tree removal, and sandbag placement.

                                  Boulder Creek (Post-Cedar Fire, September, 2004)                                 Photo by Jimmy Smith*                                  

Post-fire Impacts on the San Vicente Management Area of the Watershed

Pre-fire source water and reservoir monitoring showed the primary concerns in the San Vicente Management Area are turbidity, nutrients, bacterial indicators, and TDS.  Hazardous chemical may be present in the soil at the burned over salvage yard on the Barona Reservation; these chemicals have the potential to be transported downstream by floods and harm the environment or human health.

The San Vicente Management Area suffered moderate soil burn severity. Immediate actions taken to control the sedimentation include: culvert cleaning and replacement,  hydromulching, debris and hazardous tree removal, and sandbag placement.

Post-fire Impacts on the San Diego Management Area of the Watershed

The identified pre-fire stressors contributing to poor water quality in the San Diego Management Area include eutrophic conditions, bacterial indicators, pH, TDS, low dissolved oxygen, and phosphorus. All of these conditions may be exacerbated by sediment-laden and nutrient-loaded water that reaches this management area from the upper watershed reaches.

The San Diego Management Area suffered low to moderate soil burn intensity, and has the lowest watershed response in the SDRW. Current data do not address the mostly private lands in this management area, however, two communities, Tierrasanta and Scripps Ranch (not in SDRW), suffered severe damage from the Cedar Fire, and the City of San Diego is assisting these homeowners to reduce the impacts of erosion.  The storm drains associated with the urban communities in the San Diego Management Area empty directly into the waterways, beaches, bays, and ocean, and to maintain water quality citizens are asked to control, contain, and capture the sediment and debris.  Capturing ash, filtering stormwater before it enters the storm drain, and pumping pool water directly into the sanitary system are some of the recommendations suggested by the City of San Diego.


Turbidity/Oxygen Depletion Cycle

                                                                                                                                      Created by Heather Karnes-Schmalbach, 2005


Source: Adapted from Anchor Environmental CA, Everest International Consultants, KTU+A, Merkel and Associates, TRAC, & Welch, M. (2004, August). San Diego River watershed management plan; Baseline assessment. San Diego, CA: Project Clean Water Website, County of San Diego. Retrieved February 7, 2005 from

Photo credits:

Cuyamaca Ranch State Park Website. (2005). Pre-fire pictures. Retrieved March 21, 2005 from

*Mastrocola, M. (2005). Selected photographs. San Diego, CA: Author.

*Smith, J. (2005). Selected photographs. California Regional Water Quality Control Board, San Diego Region

*Streit, S. (2005). Bird friends of San Diego County. Retrieved January 29, 2005 from

[See also Friends of Famosa Slough at ]