Clean Water Act (CWA) Section 401


This Program regulates discharges of fill and dredged material to all waters of the state, including waters of the U.S. under Clean Water Act (CWA) section 401 and the Porter-Cologne Water Quality Control Act. Additional protections are provided for wetlands, special aquatic sites and headwaters because these waterbodies have high resource value, are vulnerable to filling, and are not protected by other programs. The Program is involved with protection of special-status species and regulation of hydromodification impacts. The Program encourages watershed-level analysis and protection, because some functions of wetlands, riparian areas, and headwater streams–including pollutant removal, flood water retention, and habitat connectivity–are expressed at the watershed or landscape level. The core of the Program's protection strategies is demonstration of impact avoidance first, followed by minimization, and then mitigation to compensate for impacts and ensure no net loss of water resources. The 401 program was allotted an addition position beginning in July 2014, so the Program is now operating with 1.8 PYs.

The Clean Water Act Program Fact Sheet provides more information on the Goals, Accomplishments, and Performance Targets.

Under federal Clean Water Act (CWA) section 401 every applicant for a federal permit or license for any activity which may result in a discharge to a water body must obtain State Water Quality Certification (Certification) that the proposed activity will comply with state water quality standards. Most Certifications are issued in connection with U.S. Army Corps of Engineer (Corps) CWA section 404 permits for dredge and fill discharges.

Starting in 2016, project applicants conducting dredge, fill, excavation or grading in waters of the state will be required to upload project information into EcoAtlas. Starting in 2017, some project applicants will be required to perform project assessments using CRAM on their project sites. Some of these projects may need pre-project CRAM assessment on their Project site performed during the summer of 2016. See EcoAtlas and CRAM.

Available Documents

  • 401 Water Quality Certification Processing Time Lines
  • Instructions for Completing Application for CWA 401 Water Quality Certification and Waste Discharge Requirements for Dredge and Fill Projects (revised posting 12/10/14)
  • New! Initial Application Fee: Please submit $1638 fee payable to “State Water Resources Control Board” with your application.
  • Lahontan Application for CWA 401 and WDR for Dredge and Fill Projects - Writeable PDF version
  • Lahontan Application for CWA 401 and WDR for Dredge and Fill Projects - Word version
  • Water Quality Certification for Discharges of Dredge or Fill Materials Under CWA Section 401
  • Lake Tahoe Dredging Study (19.89 MB)
  • Dredge and Fill Fee Calculator
  • Adopted Fee Schedule (see "Water Quality Certification" for current year)
  • Section 401 Water Quality Certification Public Notices
    The State Water Resources Control Board revised State regulations for the 401 Water Quality Certification Program; these revisions went into effect on June 24, 2000. The revised regulations [23 CCR § 3830-3869] may be found at or State 3858 (a) states:
    "The executive director or the executive officer with whom an application for certification is filed shall provide public notice of an application at least twenty one (21) days before taking certification action on the application, unless the public notice requirement has been adequately satisfied by the applicant or federal agency. If the applicant or federal agency provides public notice, it shall be in a manner and to an extent fully equivalent to that normally provided by the certifying agency. If an emergency requires that certification be issued in less than 21 days, public notice shall be provided as much in advance of issuance as possible, but no later than simultaneously with issuance of certification."
  • Pending Water Quality Certification Applications
    Selected information on pending applications currently being reviewed for consideration of Water Quality Certification under Section 401 of the Clean Water Act. The public has 21 days from the date posted to comment on projects currently under review by the Regional Board staff.
    • North Lahontan Region - Pending Applications - (WDIDs beginning with 6A)
    • South Lahontan Region - Pending Applications - (WDIDs beginning with 6B)

    • Bonnie Clare Road Reconstruction Project, Death Valley National Park, Inyo County
      The Lahontan Regional Water Quality Control Board (Water Board) intends to rely upon the Environmental Assessment (EA) and Finding of No Significant Impact (FONSI) prepared by the National Park Service (NPS) for the Bonnie Clare Road Reconstruction Project (Project). The NPS circulated the Project EA for public review in November 2017 through the State Clearinghouse (SCH) under SCH No. 2017111061. As Lead Agency for this Project under the California Environmental Quality Act (CEQA), the Water Board finds that (1) the EA/FONSI includes the elements necessary to meet the requirements under CEQA, and (2) that the NPS circulated the EA/FONSI for public review in substantial conformance with the requirements of California Code of Regulations, title 14, section 15087, title 14). Therefore, the Water Board is providing this Notice of Intent to rely on the Project EA to satisfy its environmental review obligations under CEQA in accordance with California Code of Regulation, title 14, section 15225.

      Please direct any comments or questions on the Bonnie Clare Road Reconstruction Project to Jan Zimmerman (; 760/241-7376) no later than September 14, 2018.

  • If you wish to be informed of the status and/or final certification action on any of these projects and/or for further information, please contact the staff noted below. We encourage public input during the certification process. Comments on any of these projects may be submitted in writing by email or U.S. Postal Service (see the addresses below). Project descriptions included here are provided by the applicant. These lists are updated approximately every 2 weeks.

    North Lahontan Region
    Attn: Rob Tucker - 530 542-5467
    Lahontan Regional Water Quality Control Board
    2501 Lake Tahoe Blvd.
    South Lake Tahoe, CA 96150-7704
    South Lahontan Region
    Attn: Jan Zimmerman - 760 241-7376
    Lahontan Regional Water Quality Control Board
    Our new location is:
    15095 Amargosa Rd., Bldg 2 - Suite 210
    Victorville, CA 92394