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4 November 2025

Controversy Over State And Tribal Rights Under Clean Water Act Section 401 Continues

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Ten members of Congress representing New York districts have petitioned Gov. Kathy Hochul to withhold the state's water quality certification needed for a natural gas pipeline in New York waters.
United States New York Energy and Natural Resources
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Ten members of Congress representing New York districts have petitioned Gov. Kathy Hochul to withhold the state's water quality certification needed for a natural gas pipeline in New York waters.

Section 401 of the Clean Water Act requires that States and Tribes have the opportunity to certify their acceptance of activities that may result in a "discharge" into a "Water of the United States" before the federal government issues a permit or license authorizing those activities. That certification can specify enforceable conditions beyond those the federal government might impose.

Examples of activities requiring certification include dredging, the generation of hydroelectricity, construction of gas pipelines and discharges of "pollutants" authorized by National Pollutant Discharge Elimination System (NPDES) permits, including by construction permits.

During the first Trump Administration, the U.S. Environmental Protection Agency (EPA) amended its Section 401 Water Quality Certification regulations to constrain States and Tribes from considering concerns other than regarding water quality in issuing, or refusing to issue, water quality certifications and to promote timely action on requests for Water Quality Certification by States and Tribes.

During the Biden Administration, EPA reversed itself and went a considerable distance in the opposite direction. However, in May, EPA announced its renewed position that Section 401 of the Clean Water Act "is limited to addressing only water quality-related impacts."

The letter from the 10 members of Congress makes plain that those members disagree with EPA about the reach of Section 401. The letter expresses concerns that go well beyond concerns about water quality, including whether there is a need for the pipeline in question, something the Federal Energy Regulatory Commission has already determined and determined again.

It remains to be seen whether the State of New York will continue to withhold the water quality certification required by Section 401 of the Clean Water Act for this project to proceed and, if so, on what basis.

It is also unknown when EPA will publish the regulations that will be more in line with the Water Quality Certification regulations finalized in 2020 or the extent to which those regulations will streamline the State and Tribal processes made more cumbersome during the Biden Administration.

If and when such regulations are published – and finalized – they will likely be challenged in court just like the regulations finalized during the prior Trump and Biden administrations.

If challenges to those new regulations reach the U.S. Supreme Court, one can expect that, based on the Supreme Court's recent tangles with the Clean Water Act, and its opinion earlier this year in Seven County Infrastructure Coalition v. Eagle County, the nation's highest court will favor a narrower view of the reach of Section 401.

What is certain is more uncertainty for the regulated community and more litigation as the controversy over this and other elements of the Clean Water Act continues, as it has for decades.

The content of this article is intended to provide a general guide to the subject matter. Specialist advice should be sought about your specific circumstances.

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