San Diego Region - Wetlands and Riparian Protection

The San Diego Water Board's Wetland and Riparian Protection Program (Program) seeks to preserve, protect, restore, and enhance the Region's wetlands, streams, and other aquatic resources that are waters of the United States and/or State (waters). The San Diego Water Board's ability to issue federal Clean Water Act section 401 Water Quality Certifications (Certifications) and/or waste discharge requirements via the California Water Code to applicants that condition the discharge of dredge or fill material to waters is the cornerstone of the Program. To achieve no net loss and a net gain of wetlands and other aquatic resources, applicants are expected to avoid deliberate discharges of materials into waters and then to minimize discharges that cannot be avoided. When impacts are unavoidable, applicants are required to provide "compensatory mitigation" to offset the impacts as a condition of the Certification. Compensatory mitigation attempts to recreate the structure and functions of the impacted waters through creation, re-creation, rehabilitation, and enhancement either on- or off-site.

Effective May 28, 2020, the State Water Resources Control Board adopted a State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State (Procedures). For more information, including training materials and implementation guidance, please visit the new Procedures website.

Public Notices

Public Notices

Last Updated 04/12/2021 - Water Quality Certification Notices (PDF)

State regulations require that applications for 401 Water Quality Certification are publicly noticed for a minimum of twenty one (21) days prior to the San Diego Water Board taking an action. Written comments can be sent by email, mail, or fax to the San Diego Water Board. Please include the pending certification number or place identification number in the subject line of your correspondence and send to:

California Regional Water Quality Control Board
San Diego Region
2375 Northside Drive, Suite 100
San Diego, CA 92108
Main Fax Number: (619) 516-1994

Certified Actions

Certifications issued since January 2008 can be accessed by clicking the link below. To review a certification issued prior to January 2008, please request a file review.

Denied Actions

Applications denied since January 2019 can be accessed by clicking the link below. To review denied applications issued prior to January 2019, please request a file review.

Types of 401 Certifications

The type of Clean Water Act Section 401 Water Quality Certification (or, 401 certification) depends on the project activity, location, and federal permit being sought. Please consult with San Diego Water Board staff for additional guidance.
  • Individual 401 Certification (instructions below)
  • Emergency repair projects where there is a sudden, unexpected occurrence that demands immediate action to prevent loss of life, health, property, or essential public services.
    • Review additional information and requirements for the certification for the Certification for RGP 63
    • Submit a Notice of Intent (NOI) and application fee to the San Diego Water Board
  • Small habitat restoration projects, where the primary purpose is to restore habitat and where impacts will be less than 5 acres or 500 linear feet of jurisdictional waters. Not applicable to mitigation projects.
  • Removal of invasive plants, where the project involves only the removal of invasive plants in areas that contain at least 50% cover of invasives.
    • Review additional requirements and instructions for the Certification for RGP 41
    • Submit notification and application fee to the San Diego Water Board
  • Projects that qualify for Army Corps Nationwide Permits
    • For Permit Nos. 1, 4, 5, 6, 9, 10, 11, 20, 22, 28, 32, 36, or 54
    • For Permit Nos. 12, 57 and 58
    • For all Nationwide Permits that do not qualify for coverage under a Water Board General Order, apply for an individual 401 certification from the San Diego Water Board.

Individual 401 Application Information

Step 1: Request a pre-filing meeting a minimum of 30 days before submitting an application for an individual 401 water quality certification. This meeting provides an opportunity for the applicant and Water Board staff to discuss potential water quality impacts, possible steps to avoid and minimize impacts, and review possible compensatory mitigation.

  • Requests should be made in writing, preferably on letterhead, and sent to with the subject line “Pre-filing meeting request for [Project Name], ATTN: Eric Becker”
  • Include as much of the following information as possible:
    • Name of project and project proponent [required]
    • Brief project description, including location, nature of proposed activity, and potential impacts to water quality [required]
    • Approximate timeline for project construction and operation
    • A preliminary list of other state and federal authorizations needed for the project
    • A draft figure or map of the project, illustrating proposed impacts to jurisdictional waters
    • A draft application form
  • Keep a copy of your written request, as documentation of a pre-filing meeting request must be submitted with an application for water quality certification.
  • The San Diego Water Board will not respond to all requests for pre-filing meetings. If it has been 30 days since the receipt of your request, you may submit your application for 401 water quality certification.

Step 2: Submit an Application for Individual Water Quality Certification and/or Waste Discharge Requirements.

  • Fill out an application.
  • How to submit applications:
    • Electronic applications may be sent to with “401 Application” in the subject line.
    • Documents larger than 50 MB must be saved to a disk or flash drive and delivered to the San Diego Water Quality Control Board, 2375 Northside Dr. Ste 100, San Diego, CA 92108.
    • Paper applications may be delivered to the San Diego Water Board office at the above address.
  • Send a second, identical copy of your application to the U.S. Army Corps of Engineers. Project applicants must concurrently notify the Corps and the San Diego Water Board when applying for water quality certification.

Step 3: Submit Application Fee.

  • Dredge and Fill Fee Calculator to calculate application fee
  • Pay fees via check made payable to State Water Resources Control Board and delivered to the San Diego Water Board office.
  • Pay fees online here with a credit card.

Application Guidance

    1. Project proponent and point of contact
    2. Proposed project;
    3. Applicable federal license or permit;
    4. The location and nature of any potential discharge that may result from the proposed project and the location of the receiving waters;
    5. Description of any methods to monitor, treat, control, or manage the discharge;
    6. A list of all other authorizations required for the project;
    7. Documentation that a pre-filing meeting was requested (see guidance above);
    8. This signed statement: “The project proponent hereby certifies that all information contained herein is true, accurate, and complete, to the best of my knowledge and belief.”; and
    9. This signed statement: “The project proponent hereby requests that the certifying authority review and take action on this CWA 401 certification request within the applicable reasonable period of time.

Additional Resources

The following resources may be useful in preparing an application for water quality certification.


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