401 Water Quality Certification and Wetlands Program

  Application and Guidance Materials

Application:

If you think your project qualifies for coverage under the State Water Board’s 2020 General Order for Nationwide Permits 12, 57, or 58 (Order No. [WQ] 2020-0039-EXEC), please visit the General Orders website for instructions on how to apply. See the Frequently Asked Questions below for more information.

• Application for Individual Water Quality Certification and/or Waste Discharge Requirements (MS Word)
• Application for Individual Water Quality Certification and/or Waste Discharge Requirements (PDF)
• Optional Review Checklist for Contents of a Complete Dredge or Fill Application

Regulations:

• Procedures for Discharges of Dredged or Fill Materials to Waters of the State
• California Code of Regulations Title 23. Waters Division 3. State Water Resources Control Board Chapter 28. Certifications

Guidance and Training:

• Implementation Guidance on the Procedures
• Video recording of the May 7th, 2020 public training webinar for the Procedures
  • PowerPoint presentation for the May 7th, 2020 public training for the Dredge or Fill Procedures
• Alternative Analysis Flowchart
• Staff Report – Including Substitute Environmental Documentation for the Procedures
• EcoAtlas-Watershed Profile Factsheet_2024 (sfei.org): A Watershed Profile is often required as part of an application for proposed restoration projects or mitigation for dredge or fill projects.

  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.

Do I need to request a Pre-Filing Meeting?

Applicants 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.  In some cases, the Water Board may shorten or waive this requirement; applicants should contact their local Water Board for more information.

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).

Where do I submit my application?

Regional Water Board (most applications):

Applications should be sent to the appropriate Water Board based on the location of the proposed project discharge. If the project is located fully within a Regional Water Board boundary, the application should be submitted to that Regional Water Board office. Refer to the Water Boards Map to find your local Water Board office and refer to the 401 Program Staff Directory for contact information and instructions where to send your application.

State Water Board – Division of Water Rights:

If your project involves a Federal Energy Regulatory Commission (FERC) license, an appropriation of water, or a diversion of water for domestic, irrigation, power, municipal, industrial, or other beneficial use, you must send your application to the Division of Water Rights’ 401 Certification Program. Mail your hard copy application and fee to the following address:

State Water Board – Division of Water Quality:

If your project crosses Regional Water Board boundaries and does not involve a water right or FERC license, send your application to the Division of Water Quality’s 401 Certification Program. For these projects, email your pre-filing meeting requests and applications to:

You may also mail your hard copy application and fee to:

Nationwide Permits 12, 57, and 58: 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.

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

For individual permits, Water Board staff will review applications 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 a permit (401 water quality certification or waste discharge requirements), or notify you that your application has been denied.

For enrollment under a general order, Water Board staff will review a notice of intent 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.

How long will it take to receive a permit decision for an individual permit?

Once the Water Board has determined your application complete, the time it takes to process your permit will vary based on the type of permit and scale and scope of the project. Permits for small projects with minimal impacts may be processed within 60 days, and permits for larger projects may take up to a full year to process. For information on typical process times, refer to our program's Annual Performance Report or the Memorandum of Understanding between the California Water Boards and the Army Corps of Engineers (California Districts) for reasonable period of times to act on certification requests.

  Fees

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 24/25 Water Quality Certification Dredge or Fill Fee Calculator is publicly available for informational purposes only and estimates fees in accordance with the fiscal year 2024-2025 fee schedule. The final fee amount will be determined by Water Board staff in accordance with the California Code of Regulations (section 2200).

• FY 2024-2025 Dredge or Fill Fee Calculator (Effective 10/31/2024)
• Frequently asked questions about fees
• Making an online payment

  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. View the 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.

• Currently Issued General Orders
• Emergency General Orders
• General Orders Under Development
  • Statewide Utility Wildfire General Order

  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

• Processing Applications for Development Permits Under the Permit Streamlining Act; The Permit Streamlining Act establishes time limits for public agencies' review and approval of applications for development projects. Its purpose is to ensure a clear understanding of the requirements applicants must meet and to expedite public agency decisions concerning development projects. This memo outlines how this Act applies to actions of the State and Regional Water Boards.
• In-Lieu Fee Program for the U.S. Army Corps of Engineers Sacramento District (Effective 10/10/2014) is sponsored by the National Fish and Wildlife Foundation (NFWF) is approved by federal and state agencies, including the Water Boards. The Program provides compensatory mitigation opportunity for discharges that occur within the jurisdiction of the Corps’ Sacramento District.
• RIBITS (Regulatory In lieu Fee and Bank Information Tracking System) was developed by the U.S. Army Corps of Engineers with support from the Environmental Protection Agency, the U.S. Fish and Wildlife Service, the Federal Highway Administration, and NOAA Fisheries to provide better information on mitigation and conservation banking and in-lieu fee programs across the country. RIBITS allows users to access information on the types and numbers of mitigation and conservation bank and in-lieu fee program sites, associated documents, mitigation credit availability, service areas, as well as information on national and local policies and procedures that affect mitigation and conservation bank and in-lieu fee program development and operation.
• California EcoAtlas provides access to information for effective wetland management. The maps and tools can be used to create a complete picture of aquatic resources in the landscape by integrating stream and wetland maps, restoration information, and monitoring results with land use, transportation, and other information important to the state’s wetlands. The Landscape Profile Tool provides project proponents information and data to develop a Watershed Profile, often required as part of an application for dredge and fill projects. For more information on how to use the tool, refer to Watershed Profile Factsheet 2024.
• California Wetland Monitoring Workgroup (CWMW) works to improve the monitoring and assessment of wetland and riparian resources by developing a comprehensive stream, wetland and riparian area monitoring plan for California and through increasing coordination and cooperation among local, state, and federal agencies, tribes, and non-governmental organizations.
• California Rapid Assessment Method (CRAM) is a cost-effective and scientifically defensible rapid assessment method for monitoring the conditions of wetlands throughout California. It is designed for assessing ambient conditions within watersheds, regions, and throughout the State. It can also be used to assess the performance of compensatory mitigation projects and restoration projects.
• Technical Advisory Team (TAT) Memos
  • Technical Memorandum 1: Technical Advisory Team Formation and Purpose
  • Technical Memorandum 2: Wetland Definition
  • Technical Memorandum 3: Landscape Framework
  • Technical Memorandum 4: Wetland Delineation
• Low Impact Development – Sustainable Storm Water Management
• California Department of Fish and Wildlife – Lake and Streambed Alternation Program
• U.S. Environmental Protection Agency – Region 9, Wetlands, Oceans and Watersheds – Wetlands Helpline
• U.S. Army Corps of Engineers (HQ Regulatory Program)
  

  Los Angeles District | Sacramento District  |  San Francisco District

  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.
  • Executive Order W-59-93