San Diego Region - NPDES Program

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Do I need an NPDES permit?

Do you discharge pollutants from a point source to a surface water of the United States? If so, you need a National Pollutant Discharge Elimination System (NPDES) permit.

As authorized by the Clean Water Act (CWA), the NPDES Program controls water pollution by regulating point sources that discharge pollutants into waters of the United States. Point sources are discrete conveyances such as pipes or man-made ditches. Examples of pollutants include, but are not limited to, rock, sand, dirt, and agricultural, industrial, and municipal waste discharged into waters of the United States. See section 122.2 of 40 Code of Federal Regulations (CFR) for the actual definitions of point source, pollutant, and water of the United States.

The NPDES Program is a federal program which has been delegated to the State of California for implementation through the State Water Resources Control Board (State Water Board) and the nine Regional Water Quality Control Boards (Regional Water Boards), collectively Water Boards. In California, NPDES permits are also referred to as waste discharge requirements (WDRs) that regulate discharges to waters of the United States.

Since its introduction in 1972, the NPDES Program has been responsible for significant improvements to our nation's and State’s water quality.

Who can I contact for more information?

Staff Name
Phone Number
Brandi Outwin-Beals, P.E.
Senior WRC Engineer
Joann Lim
WRC Engineer
Vicente Rodriguez
WRC Engineer
Fisayo Osibodu
WRC Engineer
James Chhor
Environmental Scientist

What is a General NPDES Permit?

The Water Boards develop and issue general permits to cover multiple facilities within a specific category. The use of general permits allows the Water Boards to allocate resources in a more efficient manner and provide timely permit coverage for large numbers of facilities in the same category. In addition, the use of a general permit ensures consistency of permit conditions for similar facilities. According to 40 CFR section 122.28, general permits may be written to cover categories of point sources having common elements, such as:

  • Storm water point sources
  • Facilities that involve the same or substantially similar types of operations
  • Facilities that discharge the same types of wastewater
  • Facilities that require the same effluent limitations or operating conditions
  • Facilities that require the same monitoring where tiered conditions may be used for minor differences within class (e.g., size or seasonal activity)
  • Facilities that are more appropriately regulated by a general permit

However, general permits may only be issued to dischargers within a specific geographical area such as the following:

  • City, County, or State boundary
  • Designated planning area
  • Sewer district
  • Standard metropolitan statistical area
  • State highway system
  • Urbanized area

A complete list of the general NPDES permits that have been issued in the State of California can be found on the State Water Board’s webpage

The following is a list of the General NPDES Permits specific to the San Diego Region:

General Regional NPDES Permits

Order Number NPDES Permit Number
Boatyards and Boat Maintenance Facilities
Groundwater Extraction
Lanthanum-Modified Clay

Shipyard Facilities
For a copy of this document, please email a request to our records administrator at

What is an Individual NPDES Permit?

An individual NPDES permit is a permit specifically tailored to an individual facility. After receipt of a complete application, the San Diego Water Board develops a permit for a particular facility based on the information contained in the application (e.g., type of activity, nature of discharge, receiving water quality) for an effective period not to exceed five years. The discharger must reapply at least 180 days prior to the expiration date.

Information regarding the permitting process and the fee schedule is available on the State Water Board's webpage

Individual NPDES Permits in the San Diego Region

Order Number Facility
BAE Systems San Diego Ship Repair
R9-2019-0167 - For a copy of this document , please send an email to
Camp Pendleton Advanced Water Treatment Plant
R9-2019-0167 - For a copy of this document , please send an email to
Camp Pendleton Southern Regional Tertiary Treatment Plant
Carlsbad Water Reclamation Facility
City of San Clemente Segunda Deshecha Runoff Plant
City of San Clemente Water Reclamation Plant
Huntington Ingalls San Diego Shipyard, Inc. ( Continental Maritime of San Diego )
El Toro Water District Water Reclamation Plant
Meadowlark Water Reclamation Plant
R9-2019-0169 - For a copy of this document , please send an email to
Fallbrook Public Water District Santa Margarita Groundwater Treatment Plant
R9-2019-0169 - For a copy of this document , please send an email to
Fallbrook Public Water District Water Reclamation Plant (formerly known as Wastewater Plant No. 1)
R9-2019-0168 - For a copy of this document , please send an email to
Genentech, Inc.
Hale Avenue Resource Recovery Facility Discharge to Pacific Ocean
Irvine Desalter Project Potable Water Treatment System
Irvine Desalter Project Shallow Groundwater Unit
Irvine Ranch Water District Los Alisos Water Reclamation Plant
R9-2019-0166 - For a copy of this document , please send an email to
La Salina Wastewater Treatment Plant
Encina Water Pollution Control Facility
Membrane Filtration/Reverse Osmosis Facility
R9-2019-0166 - For a copy of this document , please send an email to
Mission Basin Groundwater Purification Facility
National Steel & Shipbuilding Company (NASSCO)
North City Water Reclamation Plant and Pure Water Facility
Palomar Energy Center
Point Loma Wastewater Treatment Plant
Ray Stoyer Water Recycling Facility
San Elijo Water Reclamation Facility
San Juan Capistrano Groundwater Treatment Plant
R9-2019-0166 - For a copy of this document , please send an email to
San Luis Rey Water Reclamation Facility
San Onofre Nuclear Generating Station
Santa Margarita Water District Chiquita Water Reclamation Plant
Santa Margarita Water District Oso Creek Water Reclamation Plant
SeaWorld, San Diego
R9-2021-0001 as amended by R9-2023-0009

South Bay International Wastewater Treatment Plant

For a copy of this Order No. R9-2021-0001 as amended by R9-2023-0009, please send an email to

South Bay Water Reclamation Plant
South Coast Water District Aliso Creek Water Reclamation Facility (formerly known as Aliso Creek Water Harvesting Project)
South Coast Water District Doheny Desalination Project
South Coast Water District Groundwater Recovery Facility
South Orange County Wastewater Authority 3A Regional Plant
South Orange County Wastewater Authority Coastal Treatment Plant
South Orange County Wastewater Authority J.B. Latham Wastewater Plant
South Orange County Wastewater Authority Regional Treatment Plant
Stone Brewing Company
Sweetwater Authority Richard A. Reynolds Desalination Facility
U.S. Naval Base Coronado
U.S. Naval Base Point Loma
U.S. Naval Base San Diego
University of California, San Diego - Scripps Institution Of Oceanography

Additional Information

  • State Water Board NPDES Webpage - The State Water Board NPDES webpage contains links to statewide NPDES general permits, a description of the NPDES permitting process, and other information regarding the implementation of the NPDES program in the State of California.
  • U.S. Environmental Protection Agency (USEPA) NPDES Webpage - The USEPA NPDES webpage contains basic information about the NPDES permit program, and applicable federal regulations, including pretreatment and biosolids regulations.