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EPA Set to Revise Clean Water Act’s Section 401 Regulations

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The 2020 Navigable Waters Protection Rule (NWPR), commonly referred to as the 2020 Trump Rule, restricted States and Tribes authority to implement Section 401 of the Clean Water Act most notably by limiting their time frame for review and the conditions that could be imposed on federal permits. On June 9, 2022, the Environmental Protection Agency (EPA) released a proposed rule that would reverse many restrictive aspects of the NWPR and would considerably expand the States and Tribes authority in some key ways, ultimately affecting the Section 401 permitting process. Comments are being accepted on the proposed rule until August 8, 2022, and a final rule is expected in 2023. So what might this proposed rule mean for future projects and their applicants? Let’s scratch the surface!

One of the most noteworthy changes of the proposed rule is the opportunity for certifying authorities to now consider projects as a whole and how they might affect water quality. The purview of States and Tribes would now look beyond those project elements that have a direct point source discharge (i.e., direct impacts) and consider all elements of the project regardless of their location and potential to discharge into a waters or affect water quality (i.e., indirect impacts). This reviewing “projects as a whole” approach will in turn also expand the conditions which may be placed on an individual project and will no longer be restricted to the point source discharge. This likely means a return to Section 401 permits in California triggering a review of development stormwater design or other non-point source discharges. It remains to be seen what types of conditions might now be included.

Despite the return to increased purview of certifying agencies and the added complexity that may result, the new rule appears to streamline the certification timeline. The pre-application filling meeting has been retained in the proposed rule along with the one-year maximum timeline, but it now requires both the federal and certifying authority to collaboratively set the timeline. For projects in California seeking Clean Water Act Section 404 permits, the timeline will be a decision between the Corps and the Regional or State Water Board. This may eliminate the need to submit draft application materials to the certifying entity and complete consultation under draft review prior to submittal of the certification request or application. It should be noted, however, not all Regional Water Boards have chosen to implement draft reviews but knowing how favorably the San Francisco Regional Board views these, they may be here to stay for that region regardless. Dredge fill fees will likely also be set upon receipt of the certification request and not be subject to new fill fee rates should a new rate schedule be published while the certification is in consultation.

Lastly, the proposed rule requires that all certification requests submit a copy of a draft license or permit. This will undoubtedly change the approach to the permit application process and timelines so many of us are used to as this may decouple the Section 404 and 401 permitting processes. Permitting with the federal entity would need to be nearly completed first before requesting certification. For example, if a project is seeking an Individual Permit under Section 404 and Section 401 certifications, a draft of the Corps’ Individual Permit would be required to be submitted with the Section 401 Certification request. Draft permits are often not available until all consultations including those under the Endangered Species Act are complete. The EPA is requesting comments on this proposed change, and we anticipate many in California will focus comments on this item because of the potential impacts to project approval timelines.

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Permitting has always been complicated and recent court cases have added another layer of complexity in trying to navigate the requirements of the Corps and the State Water Board regions. Now we will have expanded purview of the certifying authorities, making it more difficult to anticipate conditions and requirements and potentially a decoupled permitting process. WRA permitting specialists are here to assist and are working diligently to stay on top of the ever-changing regulatory world. We will keep you informed of updates on the proposed rule. In the meantime if you’d like expert help to understand how this may affect an in-progress project or one in the planning stages, please email Bianca Clarke ( or reach out via our contact form.