Clean Water Act Section 401 Water Quality Certification Program

For additional information please select from the following links:

Permit process for:

Individual 401 Application Packet (updated in 2020):

General 401 or WDRs Applications:

Fee Schedule:

For information pertaining to the 401 Program in the North Coast Region, please contact Gil Falcone, 401 Certification Program Manager, at 707-576-2830 or Gil.Falcone@waterboards.ca.gov

For questions about Projects in Sonoma and Mendocino Counties, please contact Gil Falcone above. For questions about projects in  in Humboldt, Del Norte, Trinity and Siskiyou Counties, please contact Ryan Bey at (707) 576-2679 or Ryan.Bey@waterboards.ca.gov

Permitting information

This webpage is intended to assist the public in understanding the rules and regulations regarding proposed projects that may impact surface "Waters of the State". Waters of the State are defined as any surface water or groundwater, including saline waters, within the boundaries of the state. Examples of surface waters of the state include but are not limited to isolated wetlands, coastal wetlands and mudflats, perennial, intermittent and ephemeral streams and rivers, lakes, bays and coastal ocean waters.

Do you need a permit from the Regional Water Quality Control Board?

If your project is located within or adjacent to surface waters of the state, and the proposed project may directly or indirectly impact those waters, you are required to apply for a Water Quality Certification and/or Waste Discharge Requirements (Dredge/Fill Projects). The rules and regulations apply to all waters of the state, including isolated wetlands and stream channels that may be dry during much of the year, have been modified in the past, look like a depression or drainage ditch, have no riparian corridor, or are on private land. If you have any questions, it is a good idea to call the regulatory agencies in your area for clarification, and to avoid regulatory enforcement actions that may occur in response to proceeding with a project without the appropriate permits. If it is determined that you will need to apply for a Water Quality Certification and/or Waste Discharge Requirements (Dredge/Fill Projects) see below for instructions and permit process information.

State wetland definition and Procedures for discharges of dredged or fill material to waters of the state

Effective May 28, 2020, The State Water Resources Control Board (State Water Board) adopted a State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State (Procedures), for inclusion in the Water Quality Control Plan for Inland Surface Waters and Enclosed Bays and Estuaries and Ocean Waters of California. The Procedures consist of four major elements: 1) a wetland definition; 2) a framework for determining if a feature that meets the wetland definition is a water of the state; 3) wetland delineation procedures; and 4) procedures for the submittal, review and approval of applications for Water Quality Certifications and Waste Discharge Requirements for dredge or fill activities. Public information and resources on implementation of the Procedures can be found here: https://www.waterboards.ca.gov/water_issues/programs/cwa401/wrapp.html

Final Official Procedures Documents are here: State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State

Please be aware that these Procedures include newly clarified requirements for the state definition of wetlands, procedures for delineation, regulatory permitting framework including exclusions, additional new application materials required for individual certifications including; alternative analysis requirements, compensatory mitigation requirements and State Supplemental Dredge and Fill Guidelines.

Clean Water Act section 401 Water Quality Certification Permits

Section 401 of the CWA grants each state the right to ensure that the State's interests are protected on any federally permitted activity occurring in or adjacent to waters of the state. Anyone proposing to conduct a project that requires a federal permit or involves dredge or fill activities that may result in a discharge to U.S. surface waters and/or waters of the state are required to obtain a Clean Water Act (CWA) Section 401 Water Quality Certification and/or Waste Discharge Requirements (Dredge/Fill Projects). In California, the Regional Water Quality Control Boards are the agency mandated to ensure protection of the State's waters unless on tribal land. The most common federal permit for dredge and fill activities is a CWA Section 404 permit issued by the Army Corps of Engineers (USACE).

In the North Coast Region of California, the San Francisco Corps District is the USACE District responsible for permits and federal jurisdiction of dredge and fill activities within waters of the US. Their Regulatory programs, permits and staff contact can be found here (https://www.spn.usace.army.mil/Missions/Regulatory/). The USACE will determine if a project is within their jurisdiction, or not. This determination directly influences which corresponding permit the North Coast Regional Water Quality Control Board will issue. Please consult with the San Francisco Corps District early as this helps streamline the application process. The recent Supreme Court decision (Sackett v. EPA) might impact your project’s federal (and state) permitting requirements. To help answer questions about this decision, the State Water Board generated an FAQ that can be found here: https://www.waterboards.ca.gov/water_issues/programs/cwa401/docs/sackett-faq-external.pdf

If your proposed project has the potential to impact waters of the state in the North Coast Region and requires either a CWA Section 404 or other federal permit, the North Coast Regional Water Quality Control Board (NCRWQCB) will regulate the project and associated activities through a Water Quality Certification (401), verifying that the project activities will comply with state water quality standards. The type of 401 certification coverage depends on the type of project activity, location, and federal permit issued. If you are unsure which permit and corresponding application/Notice of Intent is appropriate for your proposed project, please consult with NCRWQCB 401 staff.  Possible 401 Water Quality Certifications include:

State Permits

If your proposed project does not require a federal permit but does include dredge or fill activities that will, or threatens to, result in a discharge  of pollutants to waters of the state, the NCRWQCB will regulate the project under its state authority (Porter-Cologne) in the form of Waste Discharge Requirements (WDRs) or Waiver of Waste Discharge Requirements permit. In addition, California Department of Fish and Wildlife (CDFW) may regulate the project through the Lake and Streambed Alteration Agreement process. CDFW issues Streambed Alteration Agreements when project activities have the potential to impact streams, rivers, or lakes.

The type of state permit coverage depends on the type of project activity, impact size and location. If you are unsure if a WDR or Waiver of WDRs is appropriate for your proposed project, please consult with NCRWQCB 401 staff.  Possible state permit coverage options may include:

California Environmental Quality Act (CEQA)

Before the NCRWQCB  can issue a permit, the project applicant must provide proof of compliance with the California Environmental Quality Act (CEQA). If CEQA analysis is required (i.e. the project is not found to be Categorically Exempt based on the current CEQA Guidelines), a local or state agency must act as the lead CEQA agency. Under CEQA the NCRWQCB exercises its authorities to require minimization and mitigation of impacts to "Waters of the State". At a minimum, any beneficial uses lost must be replaced by a mitigation project of at least equal function, value and overall area/length.

Water Quality Certification Permit Process

Prior to this formal process, NCRWQCB staff and managers participate in meetings and site visits with project proponents to develop project concepts and activities that avoid and minimize impacts to aquatic resources and when necessary, develop mitigation proposals to meet regulatory requirements.

Required pre-filing meeting request: At least 30 days prior to submitting an application for an individual water quality certification, project proponents are required to request a pre-filing meeting with Regional Water Board staff to discuss the project. Pre-filing meeting requests can be made by sending an email request to northcoast@waterboards.ca.gov. Meetings can be done virtually or in person and possibly at the project site. With the meeting request project proponents should include the project purpose and description, maps and photographs that accurately depict current site conditions, as well as a list of required state and federal permits. Maps must clearly identify all waters of the state and waters of the U.S. that may be permanently and temporarily impacted by the project. An explanation about how these impacts will be avoided, minimized and or mitigated for during and after the project must be provided.  U.S. Army Corps representatives should be invited to attend pre-filing meetings.

Step 1: Fill out the appropriate Water Quality Certification application or Waste Discharge Requirements NOI for Dredge/Fill Projects (links to both above)  

Step 2: Electronically submit the application or NOI and additional necessary documents (up to 50MBs) by emailing  NorthCoast@waterboards.ca.gov

Please mail a transmittal letter and check for the application fee (Make checks payable to: State Water Resources Control Board), as required according to the CCR 23 Section 2200 (a)(2) Fee Schedule (see fee calculator link above to calculate total), to:

North Coast Regional Water Quality Control Board
5550 Skylane Blvd., Suite A
Santa Rosa, CA 95403
(707) 576-2220

Email: NorthCoast@waterboards.ca.gov

Information about paying fees online can be found at https://www.waterboards.ca.gov/resources/fees/index.html#wdr

We are a paperless office and email submittal of application/NOI is preferred. However, if this is not feasible,  we will accept a paper hard copy with fee  at the address above. Do not email applications directly to staff.  Applications emailed directly to staff do not meet the requirements for a request for certification.

Step 3: Within 30 days of receiving your application packet, Regional Water Board staff will notify you in writing whether  it  is complete or incomplete (as described in Section 3856 of the California Code of Regulations and Procedures and the 2023 new Certification Rule).   If the package is incomplete, staff will include what additional items are required. Regional Water Board staff are happy to meet and discuss for clarity. At this point the submittal does not constitute a “request for certification”  and a reasonable period of time (RPOT) to issue the certification will not yet start. Please note: The Application review process will continue only after the required additional items are submitted to Regional Water Board staff.

Step 4: Once you have responded with the supplemental information, staff will review it to determine if the application is complete. Once deemed complete, reviewing staff will notify the applicant that the application is complete and that it constitutes a “request for certification” in accordance with the new 2023 water quality certification rule. We will notify the USACE  of the request, the date the application was completed, and will initiate the process of establishing an RPOT for us to take an action. Regional Water Board staff will issue a Public Notice, which will be posted on the NCRWQCB  website. The public notice period extends for 21 days. Public comments related to water quality will be accepted during the notice period, and will be considered during the certification determination process.

Step 5: The Executive Officer will take action within the reasonable time period agreed upon with the US Army Corps of Engineers. Actions may include signing and authorizing a Water Quality Certification or denying the certification if the application is incomplete or implementing the project would violate water quality requirements.

Step 6: After a determination is reached regarding issuance of CWA Section 401 Water Quality Certification and/or Waste Discharge Requirements (Dredge/Fill Projects), you will be notified by this office regarding the determination for your proposed project and receive a signed copy of the action.

Generally, the entire process (steps 1 – 6) takes between 2 - 6 months, so plan ahead and apply well in advance of the projected project start date.

State Permit Process (i.e. for non-federal jurisdiction projects)

Prior to this formal process Regional Water Board staff and managers participate in meetings and site visits with project proponents to develop project concepts and activities that avoid and minimize impacts to aquatic resources and when necessary develop mitigation proposals.

Step 1: Fill out the appropriate Water Quality Certification and/or Waste Discharge Requirements (Dredge/Fill Projects) application or Notice of Intent (NOI) available above electronically, or hard copy.

Step 2: Email the application or NOI and additional necessary documents (up to 50MBs) to NorthCoast@waterboards.ca.gov .

Please mail a transmittal letter and check for the application fee (Make checks payable to: State Water Resources Control Board), as required according to the CCR 23 Section 2200 (a)(2) Fee Schedule (see fee calculator link above to calculate total), to:

North Coast Regional Water Quality Control Board
5550 Skylane Blvd., Suite A
Santa Rosa, CA 95403
(707) 576-2220

Information about paying fees online can be found at https://www.waterboards.ca.gov/resources/fees/index.html#wdr

If emailing an application is not feasible, we will accept a paper hard copy of the application and fee at the address above.

Step 3: Within 30 days of receiving your draft application packet, staff will it to determine whether the application packet is complete (as described in Section 3856 of the California Code of Regulations), or if it is incomplete and what additional items are needed to continue the review process. If additional items are required, Regional Water Board staff will contact you in writing requesting specific items. Please note: The Application review process will continue after submittal of required items to Regional Water Board staff.

Step 4: The Executive officer makes a determination once the application is deemed complete. Plan ahead and apply well in advance of the projected project start date. Determinations may include enrollment in Waiver of Waste Discharge Requirements or Waste Discharge Requirements permits, dependent upon the project scope.

Step 5: After a final determination is reached regarding issuance of the appropriate permit authorizing work within waters of the state, you will be notified by this office regarding the determination for your proposed project.

Small Habitat Restoration Water Quality Certification process

Additional restoration permitting information can be found here: https://www.waterboards.ca.gov/northcoast/water_issues/programs/Restoration/

Step 1: If your project is habitat restoration within “Waters of the State” that impacts less than 5 acres and 500 linear feet, occurring over a period of less than 5 years, it may qualify for enrollment into the general 401 Water Quality Certification for Small Habitat Restoration issued by the State Water Resources Control Board in 2013. See this page to read the Certification and all requirements involved with enrollment: https://www.waterboards.ca.gov/water_issues/programs/cwa401/generalorders.html

Step 2: If your project qualifies, then fill out the Notice of Intent (NOI) for the Small Habitat Restoration certification downloadable at the link in Step 1. Hard copies can be mailed to applicants on an as requested basis. To request a copy please contact us (see contact information in Step 3).

Step 3: At least 30 days prior to activities, email the application and additional necessary documents to NorthCoast@waterboards.ca.gov . Please mail a check for the application fee (Make checks payable to: State Water Resources Control Board), as required according to the CCR 23 Section 2200 (a)(2) Fee Schedule (see fee calculator link above check the box for Restoration Projects), to:

North Coast Regional Water Quality Control Board
5550 Skylane Blvd., Suite A
Santa Rosa, CA 95403
(707) 576-2220

Information about paying fees online can be found at https://www.waterboards.ca.gov/resources/fees/index.html#wdr

Step 4: Within 30 days of receiving your application, staff will determine whether the application packet is complete, or whether additional items will be needed to complete the review process. A letter or email will be sent to you requesting additional items if your application is found to be incomplete. Staff may request a site inspection to verify project information and jurisdictional determinations.

Step 5: The Regional Water Board may, at its discretion, issue a Notice of Applicability to the applicant, indicating that the project activities are authorized under this Order. If project activities do not qualify for coverage under this Order, a Notice of Exclusion may be issued by the Regional Water Board. Project activities not qualified for coverage under this Order may require an application for individual Water Quality Certification described above.