National Pollutant Discharge Elimination System (NPDES) San Diego Region

As authorized by the Clean Water Act, the NPDES Permit 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 for the 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

If a facility discharges pollutants from a point source to a surface water of the United States, it needs a National Pollutant Discharge Elimination System (NPDES) permit.

Additional NPDES Permitting Program application 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.

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.

The individual NPDES permits issued in the San Diego region are listed below.

  • Order No. R9-2019-0169 as Amended by Order Nos. R9-2020-0193 and R9-2021-0204, NPDES No. CA0108031: Waste Discharge Requirements for the Fallbrook Public Utility District, Fallbrook Water Reclamation Plant and Santa Margarita Groundwater Treatment Plant Discharge to the Pacific Ocean through the Oceanside Ocean Outfall (for a copy of this order, please send an email to rb9_records@waterboards.ca.gov)
    • Adopted 2/12/2020
    • Effective 4/1/2020
    • Amended by Order No. R9-2020-0193 8/12/2020
    • Amended by Order No. R9-2020-0204 12/8/2021
    • Expires on 10/31/2023 (administratively extended)
  • CIWQS Facility At-A-Glance Report
  • Staff Contact: Joann Lim
  • Order No. R9-2019-0168 as Amended by Order Nos. R9-2020-0192 and R9-2021-0206, NPDES No. CA0107239: Waste Discharge Requirements for Genentech, Inc. Discharge to the Pacific Ocean through the Oceanside Ocean Outfall (for a copy of this order, please send an email to rb9_records@waterboards.ca.gov
  • CIWQS Facility At-A-Glance Report
  • Staff Contact: Joann Lim or James Chhor
  • Order No. R9-2018-0063, NPDES No. CA0109258: Waste Discharge Requirements for Liquid Stone Holdings, LLC dba Stone Brewing Co. Discharge to the Pacific Ocean through the San Elijo Ocean Outfall
    • Adopted 10/10/2018
    • Effective 12/1/2018
    • Expires on 11/30/2023 (administratively extended)
  • CIWQS Facility At-A-Glance Report
  • Staff Contact: Joann Lim or James Chhor

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:

  • Stormwater 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

Each general permit typically includes the following information:

  • How to apply for coverage under a general permit - see the "Notice of Intent" (NOI) form
  • How to request rescission from coverage - see the "Notice of Termination" (NOT) form

The general NPDES permits applicable to discharges to surface waters in the San Diego region are listed below.

  • Water Quality Order 2013-0002-DWQ, as Amended by Orders 2014-0078-DWQ, 2015-0029-DWQ, 2016-0073-DWQ, 2017-0015-EXEC, 2020-0037-EXEC, and 2022-0056-EXEC, NPDES No. CAG999005: Statewide National Pollutant Discharge Elimination System (NPDES) Permit for Biological and Residual Pesticide Discharges to Waters of the United States from Vector Control Applications (Pesticide-Weed Control Webpage)
    • Adopted 3/5/2013
    • Effective 12/1/2013
    • Expires on 11/30/2018 (administratively extended)
  • Water Quality Order 2016-XXXX-DWQ, NPDES No. CAG999006: Statewide General National Pollutant Discharge Elimination System (NPDES) Permit for Biological Pesticides and Residual Chemical Pesticide Discharges to Waters of the United States from Aquatic Animal Invasive Species Control Applications (Pesticide-Aquatic Animal Invasive Species Control Webpage)
    • Adopted 3/1/2016
    • Effective 6/15/2016
    • Expires on 3/1/2021 (administratively extended)
  • Water Quality Order 2016-XXXX-DWQ, NPDES No. CAG999007: National Pollutant Discharge Elimination System (NPDES) Permit for Biological and Residual Pesticide Discharges to Waters of the United States from Spray Applications for the California Department of Food and Agriculture (Pesticide-Spray Application Webpage)
    • Adopted 3/1/2016
    • Effective 7/1/2016
    • Expires on 6/30/2021 (administratively extended)
  • Water Quality Order 2016-0039-DWQ, as Amended by Water Quality Order 2022-0077-EXEC, NPDES No. CAG999004: Statewide National Pollutant Discharge Elimination System (NPDES) Permit for Biological and Residual Pesticide Discharges to Waters of the United States from Vector Control Applications (Pesticide-Vector Control Webpage)
    • Adopted 3/1/2016
    • Effective 7/1/2016
    • Expires on 6/30/2021 (administratively extended)
  • Order WQ 2014-0194-DWQ, NPDES No. CAG140001: Statewide National Pollutant Discharge Elimination System (NPDES) Permit for Drinking Water System Discharges to Waters of the United States
    • Adopted 11/18/2014
    • Effective 2/26/2015
    • Expires on 2/25/2020 (administratively extended)
  • Order WQ 2014-0174-DWQ, NPDES No. CAG999002: General National Pollutant Discharge Elimination System (NPDES) Permit for Discharges from Utility Vaults and Underground Structures to Waters of the United States
    • Adopted 10/21/2014
    • Effective 7/1/2015
    • Expires on 6/29/2020 (administratively extended)
  • Staff Contact: James Chhor or Vicente Rodriguez
  • Order R9-2023-0012, NPDES No. CAG039001: General Waste Discharge Requirements for Discharges from Shipyards to San Diego Bay (for a copy of this order, please send an email to rb9_records@waterboards.ca.gov)
    • Adopted 5/10/2023
    • Effective 9/1/2023
    • Expires on 8/31/2028
  • Notices of Applicability for Enrolled Shipyards
    • None
  • CIWQS General NPDES Permit Enrollees Report (see Regulatory Measure ID 453413)
  • Staff Contact: Vicente Rodriguez or Ella Knight

San Diego Water Board Contacts