Section 401 of the Clean Water Act provides that federal licenses and permits authorizing activities that include a point source discharge to the waters of the United States may only be granted after affected states have had an opportunity to review the activity and to certify that it will not cause a violation of state water quality standards. States (and some tribes with “treatment as a state”) have authority to grant or waive certification, to deny it, or to grant it subject to conditions. Water quality certification applies not only to individual permits, but also to nationwide permits issued every 5 years by the Army Corps of Engineers under Section 404 of the Act.
The U.S. Supreme Court sustained the application of Section 401 in 1994, in PUD No.1 of Jefferson County v. Washington Dept. of Ecology. The Court held that the state water quality certification applies to the entire activity, not just the discharge; and that state conditions become conditions on the federal permit or license authorizing the activity.
The federal rule governing state water quality certification was adopted in 1971 and used for the next five decades. However, it was completely rewritten by the first Trump Administration in 2020. The revised rule severely limited the scope of state review, taking the position that PUD No. 1 was wrongly decided, and that certification should apply only to the point source discharge and not to the entire activity. Although a district court vacated the Trump rule, the Supreme Court in a brief order (with four dissenters) stayed the lower court order and reinstated the Trump rule pending the conclusion of appellate review.
In 2023, after the Biden Administration engaged in its own rulemaking and issued its own rule in place of the 2020 rule, the litigation over the 2020 rule was dismissed as moot. The 2023 rule was largely based on the original 1971 rule; however, it modernized review procedures and expanded opportunities for authorized Tribes as well as states to be authorized to conduct certification. The 2023 rule was challenged by 11 states and several industry groups in the U.S. District Court for the Western District of Louisiana. This case is still pending; however, in 2024 the District Court denied plaintiffs’ motion for a preliminary injunction.
President Trump’s January 20 Executive Order 14156, Declaring a National Energy Emergency, directs federal agencies, including the U.S. Army Corps of Engineers, “to use, to the fullest extent possible and consistent with applicable law, the emergency [water pollutant discharge] Army Corps permitting provisions to facilitate the Nation’s energy supply.” The order cited “nationwide permits” issued by the Corps as well as emergencies defined by regulations as the authority for expedited action on energy-related projects.
Under the Corps’ existing regulations, emergencies require a finding by the District Engineer of “unacceptable hazard to life, a significant loss of property, or an immediate, unforeseen, and significant economic hardship if corrective action” is not undertaken within a time period shorter than the standard period for review. 33 § CFR 325.2(e)(4). The Division Engineer must “instruct” the District Engineer what procedures to apply, which must include “reasonable efforts” to receive comments from federal, state, and local agencies and the affected public. This is not carte blanche to ignore normal permitting procedures, including Section 401 water quality certifications, although it may shorten the timelines contemplated by the Corps regulations (60 days for certifications, up to a maximum of one year).
In stark contrast with emergencies, nationwide permits are issued by the Corps every five years. They cover many types of activities, are usually limited in scope and scale, and incorporate standard conditions in order to facilitate permitting. When nationwide permits (or regional permits, another type of general permit) are issued by the Corps, states must review and then grant, deny, or condition such permits before they can be used. For example, in states that have denied or conditioned water quality certifications for Corps Nationwide Permit 12, Oil or Natural Gas Pipeline Activities, reissued in 2021, the Corps must use its normal permitting procedures—or comply with the state conditions, if any. The Executive Order confers no additional authority on these whatsoever. The permits are and have been available, as written and conditioned, regardless of a Presidential declaration.
On February 19, the Corps publicly identified nearly 600 projects for potential permitting under the Executive Order but subsequently removed the list from its website. If permits are to be issued under emergency procedures, the procedures themselves must be identified and must comply with both statute and regulations. State water quality certifications will still apply.
In summary, state water quality certifications and conditions will apply to the entire activity in accordance with PUD No. 1 and the 2023 regulations. If water quality certifications are to be changed it is likely to require either an act of Congress or some attempt to resurrect the approach taken in the 2020 regulations. Section 401 rulemaking is not listed on the current EPA regulatory agenda, nor was it announced by EPA Administrator Zeldin in his March 12, 2025, deregulatory announcement. Water quality certification remains a mainstay of states’ authority under cooperative federalism as well as a foundation of many states’ wetland protection programs.