Water Quality Certification
- Joint Aquatic Resource Permit Application
- Joint Aquatic Resource Permit Application Instructions
- Section 401 Water Quality Certification Form Application (electronic version)
- Section 401 Water Quality Certification Form Application (printable version)
- Section 401 Water Quality Certification Application Instructions (Revised 12/09)
- Rapid Permit Assessment Checklist for 401 Certification
- California Wetlands Form (07/06/10)
- Instructions for California Wetlands Form
- California Wetlands Portal Fact Sheet
- California Wetlands Riparian Repair and Maintenance (short) Form (07/06/10)
- Instructions for the California Wetlands Riparian Repair and Maintenance (short) Form
- 2009 California Wetland Portal Annual Report
- 2010 California Wetland Portal Annual Report (draft 10/09/13)
- Form 200 WDR - Application for Report of Waste Discharge
- Joint Aquatic Resources Permit Application
- Dredge and Fill Fee Calculator
- Fact Sheet for Stream Maintenance and Enhancement Projects
- Learn About Section 401 Certification
- Fact Sheet for Wetland Projects
- Appendix I - Invasive Non-Native Plants
- Appendix I - References
- Appendix II - Suggestions for DOD sites
- Order No. R2-2018-0009 Waste Discharge Requirements for Overwater Structures
- Order No. R2-2018-0009 Attachment C - Notice of Intent
Clean Water Act Section 401 Water Quality Certification and/or Waste Discharge Requirements (WDRs for projects occurring in and adjacent to waters of the State)
Permits for Fill or Physical Changes to Waters
This document is intended to assist the public in understanding the rules and regulations regarding projects that may impact 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 include, but are not limited to, rivers, streams, lakes, bays, marshes, mudflats, unvegetated seasonally ponded areas, drainage swales, sloughs, wet meadows, natural ponds, vernal pools, diked baylands, seasonal wetlands, and riparian woodlands.
Any project that proposes to fill or otherwise physically alter creeks, wetlands, or other waters requires a number of federal, state and, in some cases, local permits before it can proceed. In describing the following permits, it should be recognized that impacts to "waters of the United States" and impacts to "waters of the State" might differ, due to the differing laws and regulations that address these impacts.
Federal Permits - Section 401 Certification
The Federal Clean Water Act, in Section 401, specifies that states must certify that any activity subject to a permit issued by a federal agency, such as the Corps, meets all state water quality standards. In California, the State Board and the regional boards are responsible for taking certification actions for activities subject to any permit issued by the Corps pursuant to Section 404 (or for any other Corps' permit, such as permits issued pursuant to Section 10 of the Rivers and Harbors Act of 1899). Such certification actions, also known as 401 certification or water quality certification, include issuing a 401 certification that the activity subject to the federal permit complies with state water quality standards, issuing a 401 certification with conditions, denying 401 certification, or denying 401 certification without prejudice, should procedural matters preclude taking timely action on a 401 certification application. Should 401 certification be denied, the federal permit is deemed denied also. Once it has received a complete application for 401 certification, the state must act on the application within 60 days, although it may request additional time to act from the Corps, up to one year.
Regional boards or their executive officers may issue 401 certifications. The State Board issues 401 certifications for projects that will take place in two or more regions. The regulations governing California's issuance of 401 certifications were updated in 2000, and are contained in Sections 3830 through 3869 of Title 23 of the California Code of Regulations. They are posted on the State Board's website Here. Under the current regulations, the state may no longer waive certification.
A nationwide permit (NWP) is a form of the Corps' 404 general permit, which authorizes a category of activities under the Nationwide Permit Program. 401 certification is necessary for all of the Corps' NWPs whether a project proponent must report its activity to the Corps or not. The State Board has certified a number of NWPs for all of California, subject to conditions notification requirements specified in that letter. A copy of the letter is available Here. The regional boards are responsible for issuing 401 certification for all NWPs not certified by the State Board.
State Permits - Waste Discharge Requirements
Under California's Porter-Cologne Water Quality Control Act (Porter-Cologne), the regional boards regulate the "discharge of waste" to "waters of the state". All parties proposing to discharge waste that could affect waters of the state must file a report of waste discharge with the appropriate regional board. The regional board will then respond to the report of waste discharge by issuing waste discharge requirements (WDRs) in a public hearing, or by waiving WDRs (with or without conditions) for that proposed discharge.
Both of the terms "discharge of waste" and "waters of the state" are broadly defined in Porter-Cologne, such that discharges of waste include fill, any material resulting from human activity, or any other "discharge" that may directly or indirectly impact "waters of the state". While all "waters of the United States" that are within the borders of California are also "waters of the state", the converse is not true - "waters of the United States" is a subset of "waters of the state."
It is important to note that, while Section 404 permits and 401 certifications are required when the activity results in fill or discharge directly below the ordinary high water line of waters of the United States, any activity that results or may result in a discharge that directly or indirectly impacts waters of the state or the beneficial uses of those waters are subject to WDRs. In practice, most regional boards rely on applications for 401 certification to determine whether WDRs need also be issued for a proposed project. The San Francisco Bay Regional Board has produced a combined 401 certification/waiver of WDRs application form to ensure that applicants do not need to file both a report of waste discharge and an application for 401 certification.
SWANCC In 2001
The U.S. Supreme Court Case (Solid Waste Agencies of Northern Cook County vs. U.S. Army Corps of Engineers, now commonly referred to as "SWANCC") ruled that isolated wetlands are not "waters of the United States", are not subject to section 404 permits or 401 certification, and should be instead regulated under state law. In California, Porter-Cologne is the state law that would regulate such waters. The Court's ruling has no bearing on the Porter-Cologne definition [of waters of the state] and the State retains authority to regulate discharges of waste into any waters of the state, regardless of whether the COE has concurrent jurisdiction under section 404.
While not a water quality permit, the California Environmental Quality Act (CEQA) requires that project proponents study and disclose a project's anticipated water quality and other environmental impacts and specify means to avoid or minimize those impacts. A proponent for any project needing state or local agency approval must comply with CEQA or indicate that its project is exempt from CEQA, pursuant to the exemptions described in CEQA regulations. A complete description of CEQA is available Here. The Regional Board must review a final CEQA document prior to taking an action on an application for water quality certification and/or WDRs.
Contact Persons:For assistance, please contact the technical staff representative listed below for the county in which the project is located:
- Regional Program Lead - Keith Lichten (510) 622-2380
- Alameda - Brian Wines (510) 622-5680
Alameda Flood Control District Permits - Leslie Perry (510) 622-2312
- Contra Costa - Katie Hart (510) 622-2356
- Marin - Nicole Fairley (510) 622-2424
- Napa - Agnes Farres (510) 622-2401
- San Francisco - Fred Hetzel (510) 622-2357
- San Mateo - Katie Hart (510) 622-2356
- Santa Clara - Brian Wines (510) 622-5680
Santa Clara Valley Water District Permits - Susan Glendening (510) 622-2462
- Solano - Agnes Farres (510) 622-2401
- Sonoma - Nicole Fairley (510) 622-2424
Sonoma County Water Agency - Xavier Fernandez (510) 622-5685
- CalTrans Permits - Derek Beauduy (510) 622-2348
- Dredging Permits - Elizabeth Christian (510) 622-2335
- Region-Wide Wetland Permits - Elizabeth Morrison (510) 622-2330