Water Quality Permits

​​On Sept. 11, 2020 the U.S. Environmental Protection Agency’s Clean Water Act Section 401 Certification Rule (40 CFR Part 121) updated and clarified the procedural requirements for water quality certification under Section 401 of the Clean Water Act, became final. Additional information, including the full text of the final rule, is available on EPA’s website. Detailed instructions for how to submit applications to DEQ can be found on the 401 Program’s 401 Certification Process page.


Program updates

On Monday June 22, the new Navigable Waterways Protection Rule took effect. Anyone with a project that could impact water quality must submit a copy of a project plan to DEQ for review and evaluation of compliance with state water quality standards, regardless of the federal jurisdictional determination, as state water quality standards still apply state-wide. If you believe your project may be impacting waters of the state, such as manipulating wetlands or waterways, or if you are submitting an application for a permit through the US Army Corps of Engineers or the Department of State Lands, regardless of federal jurisdiction, send a copy your application to the 401 Water Quality Certification Program.

DEQ will evaluate your project to determine whether a water quality review is necessary. DEQ’s project review will provide applicants with a regulatory determination and assurance of compliance with state water quality standards.

Program overview 

The 401 Water Quality Certification Program reviews and evaluates the water quality impacts of projects which require a federal permit or license to conduct any activity that may result in a discharge (including dredge and fill material) in waters of the United States under Section 401 of the Clean Water Act.


Section 401 of the CWA gives states and tribes the authority to issue state water quality certifications for projects that require a federal license or permit that may result in a discharge to waters of the US. The certification states that the discharge will comply with applicable provisions of the CWA, including state water quality standards. Oregon’s water quality standards specify the designated use of a waterbody (e.g., for water supply or recreation), pollutant limits necessary to protect the designated use (in the form of numeric or narrative criteria), and policies to ensure that existing water uses will not be degraded by pollutant discharges.

The federal permit or license cannot be issued until a 401 WQC is received.

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Regulatory authority

Regulatory authority is given to states and tribes directly through Section 401 of the CWA. Oregon Revised Statutes (ORS) 468 and 468B contain the codified body of statutory law that pertains to environmental quality and water quality for DEQ. The Oregon Administrative Rules (OAR) builds upon the ORS. OAR Chapter 340 Division 48, provides information specific to the 401 WQC program. State water quality standards are outlined in OAR Chapter 340 Division 41. Projects authorized under a 401 WQC must meet these standards.

Permit types

DEQ works closely with the U.S. Army Corps of Engineers. The USACE determines whether a project will be reviewed under an Individual, Regional General Permit or Nationwide Permit.

  • Individual Permits are for projects that have more than minimal impacts and have both general and project-specific conditions to ensure that the project can meet State water quality standards. These projects are assessed a review fee based on project complexity and anticipated review time.

  • Regional General Permits are developed for projects with recurring activities at a regional level that have impacts to a specific geographic area. Each RGP has specific terms and conditions, all of which must be met for project-specific actions to be verified. Current RGPs can be found on the USACE Portland District website. DEQ currently has 401 pre-approval in place for RGP-4 and RGP-6. 
  • Nationwide Permits are for projects that have minimal impacts and that qualify for the Nationwide 401 Water Quality Certification. There is a fee of $985 for this Nationwide certification. Projects that have new or an increase in impervious surface must submit a post-construction stormwater management plan for review and approval from DEQ prior to the start of the project. Additionally, a Land Use Compatibility Statement (LUCS) is required to be submitted.

Reducing impacts to water quality

The 401 Water Quality Certification has several tools available to ensure that a project meets state water quality standards.A WQC includes conditions that require the applicant to follow certain best management practices and perform monitoring to ensure that water quality standards are met. If there are unavoidable impacts to waterways and/or wetlands, projects are required to provide mitigation for the loss of water quality functions. Applicants may either submit a mitigation plan or purchase mitigation credits from an approved mitigation bank.

​Program contacts


Nationwide certifications

Individual certifications Northwest and Eastern Region

Individual certifications Western Region

Map of DEQ Offices