Section 401 Water Quality Certification

Regional Water Quality Control Board (RWQCB) - Section 401 (Clean Water Act) Water Quality Certification


  • Activities subject to this type of permit include any activity that would result in the placement of structures or dredged or fill materials into waters of the state, which generally encompass waters of the United States.
  • Section 401 Water Quality Certification is a requirement of the Clean Water Act that corresponds with a Section 404 Department of the Army Permit. If a Section 404 permit is being sought, Section 401 Water Quality Certification must also be sought.
  • Although Water Quality Certification must be sought for the same effects to waters of the United States as indicated in a Section 404 permit, certification can also cover effects to waterbodies that are not USACE jurisdictional (i.e., isolated wetlands).
  • Water Quality Certification is typically valid for 5 years. To learn more about water quality certification, click here.

Section 401 Water Quality Certification General Process and Steps

To apply for Section 401 Water Quality Certification, one typically follows the steps below:

  1. Prepare and submit to RWQCB a copy of the jurisdictional delineation of waters of the United States, including wetlands, that is prepared for USACE – The delineation should be conducted to determine the extent of waters of the United States, including wetlands, within the project action area. However, RWQCB also takes jurisdiction of surface waters that are outside of the jurisdiction of USACE (waters of the state). Thus it is important to make sure the delineation covers all surface water features within the project area.
  2. Prepare a project description – Prepare a written description of the project that covers the project features and activities and proposed construction methods in detail. The project description typically contains information about the location of the activities, what the project features and activities will consist of, how the activities will be conducted, what equipment and materials will be needed for the activities, how access to the site will be achieved, and the schedule of activities.
  3. Prepare location maps of the project site – prepare maps showing the project site with a clear project boundary relative to a USGS topographic quadrangle or aerial photograph, including landmark information like street names or other features to identify the location. Include the USACE delineation information on the maps if available.
  4. Prepare the Section 401 permit application – Along with the application form, RWQCB requires copies of the applications for a DFG Streambed Alteration Agreement and USACE Section 404 permit, a copy of the wetland delineation (if verified, the USACE verification letter, otherwise the delineation report), and a copy of any CEQA document prepared for the project (typically, RWQCB accepts a copy of the Notice of Determination on the CEQA document). If the document has not yet been certified or adopted, send a copy of the most completed version of the document.
  5. This permit requires a fee. Fees typically consist of a $500 base fee with additional fees added depending on the type of work and the effects to waters of the United States. A fee calculator, created by the RWQCB, is used to determine the total fee. The fee calculator can be found here.


Water Quality Certification can typically be expected within 90 days of submittal of the application. Within 30 days of submittal of the application, RWQCB will send the applicant a letter stating that the RWQCB has examined the application and is considering it either complete or incomplete. If the application is determined to be incomplete, the letter will state the items required for completion. These items must be submitted to RWQCB for the application to be considered complete and ready for processing. Once the application is considered complete, RWQCB has 60 days to issue the certification.