401 Water Quality Certification and Wetlands Program

401 Water Quality Certification and Waste Discharge Requirements


This Program is responsible for regulating discharges of dredged or fill material to waters of the state. The State Water Resources Control Board (State Water Board) and the Regional Water Quality Control Boards (Regional Water Boards) (collectively Water Boards) have the authority to regulate these discharges under section 401 of the Clean Water Act (CWA) and the Porter-Cologne Water Quality Control Act (Porter-Cologne).

CWA section 401 water quality certifications are issued to applicants for a federal license or permit for activities that may result in a discharge into waters of the United States (U.S.), including but not limited to the discharge or dredged or fill material. Waste discharge requirements  under Porter-Cologne are issued for discharges of dredged or fill material to waters of the state.

On April 2, 2019, the State Water Board adopted the State Wetland Definition and Procedures for the Discharge of Dredged or Fill Material to Waters of the State (Procedures). The Procedures became effective May 28, 2020. Applicants proposing to discharge dredged or fill material are required to comply with the Procedures unless an exclusion applies, or the discharge qualifies for coverage under a General Order.

This website provides resources and guidance for filling out and submitting applications, and other relevant program information.


  • NOTICE: June 30, 2021: The State Water Board is accepting comments on the Proposed Order for Clean Water Act Section 401 Water Quality Certification and Waste Discharge Requirements for Restoration Projects Statewide and the draft Environmental Impact Report.  View the Notice and documents for public review.
  • NOTICE: April 6, 2021: the State Water Resources Control Board adopted a resolution to confirm that the “State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State” is in effect as state policy for water quality control. Click here to view the final resolution and related documents.
  • POSTPONED NOTICE OF OPPORTUNITY FOR PUBLIC COMMENT AND NOTICE OF ADOPTION MEETING: Consideration of a Memorandum of Understanding with the California High-Speed Rail Authority to provide expedited review of project applications in accordance with the State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State. Click here to view the Revised Notice and Draft Memorandum of Understanding.

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For questions about the Procedures or general orders, contact us by email or phone at:

For project-specific, region-specific, or reporting questions, use the staff directory to contact staff at your local Regional Water Board.

State Board Program Leads

  • Dredge or Fill Procedures, Federal Coordination, General Administration:
    Beth Payne, Senior Environmental Scientist
    Wetlands Permitting and Planning Unit
    Email: Elizabeth.Payne@waterboards.ca.gov
    Phone: (916) 341-5579
  • Transportation, Restoration, Enforcement:
    Jessica Nadolski, Senior Environmental Scientist
    Wetlands Permitting and Enforcement Unit
    Email: Jessica.Nadolski@Waterboards.ca.gov
    Phone: (916) 341-5290
  • Utilities, Nationwide Permits, Fees, Enforcement:
    Jean Bandura, Senior Environmental Scientist
    Wetlands Permitting and Enforcement II Unit
    Email: Jean.Bandura@waterboards.ca.gov
    Phone: (916) 322-7781

  Frequently Asked Questions

Do I need to submit an application?

If your project may result in a discharge of dredged or fill material (as defined in the Procedures section V) to waters of the state, then you need to submit an application with the State or Regional Water Board. Discharges of dredged or fill material often occur when work is conducted in waters. Examples include, but are not limited to, development projects that fill in a water, dredging to maintain channel capacity, and activities that change the volume, grade, or capacity of an aquatic resource.

What is a Pre-Filing Meeting?

Under the new Clean Water Act Section 401 Certification Rule (effective September 11, 2020), you are required to request a “Pre-filing Meeting” with the appropriate Water Board a minimum of 30 days prior to submitting an application for an individual Clean Water Act section 401 water quality certification (40 CFR Part 121).  We encourage you to include a draft application with your request for a Pre-Filing Meeting.

For more information on the Clean Water Act Section 401 Certification Rule, visit the EPA’s webpage.

How do I apply for a 401 water quality certification or waste discharge requirements?

If your project qualifies under the terms and conditions of a general order, follow the application instructions in the applicable general order.  An application to enroll under a general order is called a notice of intent.

If your project does not qualify under the terms and condition of a general order, then you must apply for an individual water quality certification or waste discharge requirements (also called an individual order). If you are applying for an individual water quality certification, include with application documentation verifying that you requested a Pre-Filing Meeting at least 30 days before submitting your application.

Where do I submit my application?

Applications should be sent to the appropriate Water Board based on the location of the proposed project discharge. Cal. Code of Regs, section 3855. If the project is located fully within a Regional Water Board boundary, the application should be submitted to that Regional Water Board office. If the project crosses Regional Water Board boundaries, the application should be submitted to the State Water Board. Refer to the Water Boards Map to find your local Water Board office and contact information.

Note: if your project qualifies for coverage under the State Water Board’s General Order for Nationwide Permits 12, 57, or 58 (Order No. [WQ] 2020-0039-EXEC], submit your notice of intent and fee to the State Water Board per the instructions in Attachment A of the General Order.

For State Water Board applications, mail your application and fee to:

State Water Resources Control Board, Division of Water Quality
1001 I Street; 15th Floor
Sacramento, CA 95814

What happens after I submit my application or notice of intent?

Water Board staff will review applications for individual orders within 30 days of receipt and notify you if your application is complete or incomplete and if additional information is needed. Once all information has been received, the Water Boards will determine whether your proposed project will be authorized and will issue an individual order (401 water quality certification or waste discharge requirements), or notify you that your application has been denied. Water Board staff will review a notice of intent to enroll under a general order within the time frame specified in that general order. You will be notified if additional information is needed or if a notice of applicability will be issued authorizing your project.

For information on typical process times, please refer to our program’s Annual Performance Report.


Fees are assessed based on the nature of the dredge or fill discharge and the project type. The main discharge categories are:

  • Fill & Excavation Discharges – Flat application fee, a project fee calculated using impact area (both temporary and permanent impacts), and a flat annual fee.
  • Dredging Discharges – Flat application fee, annual fee calculated using dredged volume in cubic yards from previous year using the current fiscal year fee schedule.
  • Sand Mining Discharges, Ecological Restoration and Enhancement Projects, Emergency Projects authorized by a Water Board General Order, and Low Impact Discharges - Flat application fee and flat annual fee.

The FY 20/21 Water Quality Certification Dredge or Fill Fee Calculator is publicly available for informational purposes only and estimates fees in accordance with the fiscal year 2020-2021 fee schedule. The final fee amount will be determined by Water Board staff in accordance with the California Code of Regulations (section 2200).

  Public Notices

Water Code section 13167.5 requires draft waste discharge requirements be made available to the public for a 30-day comment and review period before the draft Order is considered for Board adoption. The California Code of Regulations, title 23, section 3858 requires public notice of an application for a 401 water quality certification for at least twenty one (21) days before taking action on the application, unless the public notice requirement has been adequately satisfied by the applicant or federal agency. Interested parties can subscribe to the CWQ401-Certification and Wetlands Program email list under "Water Quality" to receive updates about the Program, including public notices. Click here for public notices.

  General Orders

General Orders are issued to regulate classes of activities that are similar in nature and have minimal impacts to aquatic resources. General Orders serve to streamline the application process. Examples include certification of Corps’ regional general permits (including those for emergency activities), a subset of Nationwide Permits, and habitat restoration activities.

  State Water Board Issued Individual Orders

Projects that involve discharges to waters of the state in more than one region are under the jurisdiction of the State Water Board. Individual Orders issued by the State Water Board are located on the individual orders webpage.

  Other Resources

  Program History and Development

  • Procedures - Policy Development and Adoption
  • California Wetland Program Plan 2017 – 2022 (available upon request)
    This plan describes wetland program development activities by signatory agencies for the purposes of developing future collaborative funding through U.S. EPA Wetland Program Development Grants and other sources.
  • California State Auditor Report 2012-120 that included recommendations to improve the water quality certification program. This summarizes staff responses to the State Auditor's recommendations and will be updated periodically as additional progress is made.
  • Program Scope and Strategy, December 19, 2002 (available upon request)
  • Historical Annual Reports for 2008, 2007, 2006, 2005, 2004, 2003 (available upon request)
  • Executive Order W-59-93 (signed by Governor Pete Wilson on August 23, 1993) established state policy guidelines for wetlands conservation. The primary goal of this policy is to ensure no overall net loss and to achieve a long-term net gain in the quantity, quality, and permanence of wetland acreage in California. The federal wetlands policy, representing a significant advance in wetlands protection, was unveiled by nine federal agencies on August 24, 1993.