EPA Proposes Changes to Provide More Certainty for Clean Water Act Section 401 Water Quality Certification Review

On January 13, 2026, the U.S. Environmental Protection Agency (EPA) announced a proposed rule to revise the Clean Water Act (CWA) Section 401 water quality certification regulations (40 C.F.R. Part 121), which proposes several clarifications to enhance certainty for project applications regarding the timing and contents of applications to state certifying authorities.[1] Administrator Lee Zeldin said the proposal is intended to return Section 401 to “clear statutory boundaries” while ensuring protections are implemented “lawfully” and “efficiently.” The proposed rule would narrow the scope of Section 401 review to point source discharges, standardize what qualifies as a complete certification request and when the review clock begins, prohibit withdrawal-and-resubmittal tactics, and add transparency requirements for certification decisions and conditions.[2] The proposed rule aims to limit tactics that have become common in certain states as they attempt to gain additional time for reviewing project applications, beyond the one-year maximum provided by statute.

Context

CWA Section 401 requires a state or authorized Tribe to provide water quality certification for an activity resulting in a discharge to Waters of the United States (WOTUS) before a federal agency may issue a license or permit for that activity. By statute, the state or Tribe must act within one year or the right to review is waived. For years, project applicants have faced uncertainty from variations in approach across jurisdictions, where states have differed in their views of what starts the one-year statutory clock and whether applicants may be required to withdraw and resubmit their application to restart the clock. Challenges to these state approaches have had mixed success when challenged in court.

Also, the rules governing Section 401 certification have seesawed in recent years as federal administrations have sought to provide varying degrees of authority and flexibility to states and Tribes in issuing certification. In 2023, the EPA under President Biden issued its “Water Quality Certification Improvement Rule,” which offered minor changes to improve certainty in the application process and provided more flexibility to states or Tribes to consider water quality impacts from the broader federally permitted “activity” involved in a project application—compared with, more narrowly, water quality impacts from specific point-source discharges. The 2023 rule thereby reversed changes the previous Trump administration made in 2020 to cabin the scope of certification and related conditions imposed by the state or Tribe in the federal permit.

Key Updates

In its current announcement, the EPA states that the 2023 rule expanded the scope of Section 401 and enabled protracted timelines and “delay tactics.” EPA emphasizes that it is now proposing a rule to operate “within the clear boundaries established by Congress” for certification review, and frames the proposal as restoring Section 401 to its “proper statutory purpose” while improving permitting efficiency and reducing delays for “critical infrastructure projects.”

The major elements of the EPA’s proposal include:

A narrower scope of review focused on point-source discharges. EPA proposes to revise 40 C.F.R. § 121.3 to specify that “[t]he scope of a Clean Water Act section 401 certification is limited to assuring that a discharge from a federally licensed or permitted activity will comply with applicable and appropriate water quality requirements.” The “discharge” language is key to cabin the scope of review—i.e., to ensure review is limited to point source discharge-related impacts as opposed to broader project-related impacts.

Standardized “completeness” determination to start the one-year clock for review. EPA proposes a single list of contents needed for all certification requests, which aims to increase certainty for applicants, federal agencies, and certifying authorities about when an application is complete and therefore when the statutory clock begins to run. The proposed rule, 40 C.F.R. § 121.5, would require that all requests be “in writing, signed, and dated by the applicant.”

At a minimum, applicants are required to provide a copy of the federal license or permit application, and these additional items where applicable: readily available water quality-related materials regarding potential discharges that informed the application, and specified “additional project information,” including a description and location of proposed discharges, a map or diagram, the current site conditions, and documentation of the pre-filing meeting request (unless waived).

Prohibition on withdrawal and resubmittal of applications. The proposed rule would also add regulatory text stating that a “certifying authority may not request the applicant to withdraw a request for certification” and may not “extend the reasonable period of time other than specified in 40 CFR 121.6(d),” with any extension not exceeding one year from receipt of the request. EPA proposes removing the 2023 rule’s “automatic extension” provision tied to public notice procedures or force majeure events and instead points applicants to rely on the joint extension process (i.e., an extension of the certifying authority’s “reasonable period of time” only if the federal licensing/permitting agency and the certifying authority agree in writing, and only so long as the extension does not push the total review period beyond one year from the date the certification request was received. ___). This could significantly limit states using withdrawal-and-resubmittal tactics to avoid waiving their right to review, despite taking longer than the one year provided by statute.

Added transparency for certification decisions and conditions. EPA proposes to define certain contents that must be included in certification decisions so that applicants, federal agencies, and the public can more clearly understand the certification process, including for conditions. These include (1) a written decision that clearly identifies the type of action taken (e.g., grant, grant with conditions, denial, or express waiver) and the applicable federal license or permit, (2) a statement indicating whether the discharge will comply with “water quality requirements,” and (3) for conditional certifications, an explanation of why each condition is necessary to ensure compliance, plus a citation to the specific water quality requirement on which the condition is based. The final point is helpful for applicants who wish to challenge the decision, often a denial.

Revisions to modifications and the Section 401(a)(2) “neighboring jurisdiction” process. Under the EPA’s current regulations, a certifying authority may modify a granted certification (typically to adjust conditions to reflect discrete project changes), but the modification may not be unilateral or convert a grant into a denial. EPA now proposes to “enhance engagement” by requiring that any modification occur only if the certifying authority and the applicant all agree in writing, thus requiring the certifying authority to obtain the applicant’s agreement on the modification language. Additionally, Section 401(a)(2) provides a mechanism for an affected “other State” to object to a federally licensed or permitted activity if the discharge may affect its water quality. If the other State timely objects and requests a hearing, the federal agency must hold a public hearing and consider the EPA’s recommendations and the evidence presented before deciding whether to condition the federal authorization. EPA proposes to make this process more predictable by imposing a firm timeline: 90 days from receipt of the objection for the federal agency to notice and hold the public hearing and resolve the objection. It also seeks comment on alternatives designed to keep the overall process within a one-year window.

Submission of Comments on the EPA’s Proposal

EPA will accept comments through February 17, 2026, and requests that comments be submitted in writing and identified with Docket ID No. EPA-HQ-OW-2025-2929. . Comments can be sent via the Federal eRulemaking Portal, email (OW-Docket@epa.gov), or mail. EPA also states it will host a virtual public meeting on January 28, 2026, and that it intends to finalize the rule in Spring 2026. Project developers and other regulated entities should:

• Evaluate the EPA’s proposed changes to frame certification review in terms of point-source discharges and determine whether any adjustments should be proposed based on experience in dealing with state/Tribe certifying authorities. This is particularly important for applicants in states that have historically performed certification review—and imposed permit conditions—based on a broader framing of the requirements.
• Assess whether to submit comments on key components and/or more targeted components of the proposal to delivery greater predictability for project approval and timelines, including the EPA’s proposal around what constitutes a complete request, when the statutory clock starts, what “applicable and appropriate water quality requirements” means in practice, among other items.
• Consider impacts on applications currently being reviewed and whether any state requests for withdrawal and resubmission remain appropriate. Also consider the timing of new project submittals in relation to the EPA’s timeline for approving the new Section 401 rule.
• Assess opportunities for modifying permit conditions in current projects or projects that will require renewed/modified permitting, and whether any corresponding changes to the proposed rule are needed.

[1] U.S. EPA, Press Release: EPA Proposes CWA Section 401 Rule to Streamline Permitting, Unleash Economic Growth, and Protect America’s Waterways (Jan. 13, 2026), https://www.epa.gov/newsreleases/epa-proposes-cwa-section-401-rule-streamline-permitting-unleash-economic-growth-and.

[2] U.S. EPA, Fact Sheet: Proposed Rule: Clean Water Act Section 401 Water Quality Certification (Jan. 13, 2026).

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