EPA Clarifies Clean Water Act Section 401 Certification

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Emphasizing Water Quality and Project Certainty

On May 21, 2025, the U.S. Environmental Protection Agency (EPA) released a memorandum clarifying the appropriate use of Clean Water Act (CWA) Section 401 certifications. This memo serves as a timely reinforcement of the EPA’s longstanding position: Section 401 is a tool for protecting water quality, not a mechanism for obstructing projects based on unrelated concerns such as air emissions, traffic congestion, noise, economic preferences, or general project opposition.

Big Picture Takeaways

As the U.S. undertakes substantial investments in infrastructure, spanning energy, mineral development, transportation, and utilities, the EPA's clarification sends a clear message: Section 401 certifications must be grounded exclusively in water quality considerations. While the May 2025 memorandum does not propose regulatory changes, it reaffirms the agency’s commitment to limiting the use of Section 401 to its statutory purpose, thereby minimizing unnecessary barriers to project development.

The memo confirms that certification decisions:

  • Must be directly linked to compliance with water quality standards, and

  • Cannot be based on speculative or unrelated concerns such as air emissions, traffic, noise, or general opposition to a project.

Although the memo does not explicitly address environmental justice (EJ), it is clear that the current EPA does not consider EJ concerns within the scope of Section 401 certifications.

EPA’s Deregulatory Agenda Under the Trump Administration

This clarification supports the EPA’s broader "Powering the Great American Comeback" initiative, which aims to balance environmental protection with economic growth. On March 12, 2025, Administrator Lee Zeldin announced what the agency called the most significant deregulatory action in U.S. history. The initiative includes 31 actions designed to reduce regulatory costs, expand domestic energy production, and revive the manufacturing and auto sectors.

These actions involve reconsidering environmental regulations enacted under previous administrations, curtailing programs addressing climate and equity, and expanding states’ authority in environmental decision-making, all of which underscore the agency's commitment to streamlining permitting and certification processes.

Purpose of the May 21, 2025, Memo

The EPA issued this memorandum to clarify confusion and address stakeholder concerns regarding how Section 401 certifications are applied, especially following the 2023 regulatory update. The agency emphasized that states and authorized Tribes should not delay or deny federal permits based on issues outside of water quality. The memo reiterates that the core purpose of Section 401 is to ensure federally permitted activities do not violate applicable water quality standards.

Policy Implications

This clarification holds important implications for project developers, regulators, and federal permitting agencies. It aims to:

  • Prevent misuse of the certification process, and

  • Promote efficient, timely decision-making focused solely on water quality impacts.

The memo aligns with the March 2025 deregulatory announcement, reinforcing the narrow interpretation of Section 401 and facilitating a smoother, more predictable permitting process.

Background and Examples of Affected Permits

Federal permits commonly requiring Section 401 certification include:

  • CWA Section 404 permits for discharges of dredged or fill material (issued by the U.S. Army Corps of Engineers),

  • Hydropower and interstate natural gas pipeline licenses (issued by the Federal Energy Regulatory Commission)

  • CWA Section 402 NPDES permits (in EPA-administered jurisdictions),

  • Rivers and Harbors Act permits, including those under Sections 9 and 10.

In these cases, certification authorities — typically state environmental or water quality agencies — evaluate whether the project complies with water quality standards. Their role, while important, is deliberately limited.

Key Clarifications in the 2023 Rule

The memo highlights key principles from the 2023 EPA Rule on Section 401:

  • Certification authorities must determine whether a proposed activity will comply with specific, applicable water quality standards.

  • Conditions or denials based on generalized or unrelated concerns, such as noise, traffic, or economic effects, are not legally valid.

  • This regulatory clarity provides greater consistency and predictability for all stakeholders involved in the federal permitting process.

Next Steps and Public Engagement

To further refine the implementation of the 2023 Rule, the EPA plans to issue a notice in the Federal Register and launch a recommendations docket to solicit public input from states, Tribes, industry representatives, and other stakeholders.

These steps will inform potential updates to EPA guidance or future rulemaking aimed at ensuring consistent application of Section 401.

Legal Considerations

The May 2025 memo is a non-binding guidance document. While it clarifies and directs policy, it does not create new legal obligations or override existing statutes or regulations. In the event of a conflict, applicable laws and regulations take precedence.

Conclusion

The EPA’s latest memorandum reaffirms a focused, water-quality-driven interpretation of Section 401. This clarification enhances regulatory certainty and reduces delays for project developers and agencies navigating the federal permitting process.

If your project involves federal permitting and may require Section 401 certification, KERAMIDA’s regulatory experts are here to help. Our team understands the complexities of Section 401 and can guide you through the permitting process efficiently and in full compliance with current EPA guidance. Let us help you avoid delays and achieve successful project outcomes. Contact us or call (800) 508-8034 to speak with one of our regulatory professionals today.

Author

Wesley Fleming, MBA, PE
Senior Vice President, Operations
KERAMIDA Inc.

Contact Wesley at wfleming@keramida.com

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