PERSPECTIVE: THE SCOPE OF THE ENVIRONMENTAL PROTECTION AGENCY’S AUTHORITY UNDER §1311 OF THE CLEAN WATER ACT

The question presented in City and County of San Francisco v. Environmental Protection Agency (2025) is whether “the challenged limitations violate the Clean Water Act, by failing to identify specific limits to which petitioner’s pollutant discharges must conform[1].”

The Supreme Court’s ruling in this case addressed the Environmental Protection Agency’s (EPA) regulatory authority under the Clean Water Act; a comprehensive water quality statute that generally prohibits “the discharge of any pollutant by any person[2].”

The Clean Water Act states:

It is the policy of Congress to recognize, preserve, and protect the primary responsibilities and rights of States to prevent, reduce, and eliminate pollution to plan the development and use of land and water resources…[3].

The Act defines the term discharge of a pollutant to include “any addition of any pollutant to navigable waters from any point source,” and defines the term “pollutant” to mean, among other things, solid waste, sewage, garbage, chemical waste, biological materials, industrial, municipal, and agricultural waste discharged into surface waters[4].

The Clean Water Act requires cities to acquire a National Pollutant Discharge Elimination System (NPDES) for such discharges. The EPA established the National Pollutant Discharge Elimination System as a national approach to maintaining water quality standards. This permitting framework allows the discharge of pollutants as an exception to the above-mentioned prohibitions. Under this program, the EPA may issue permits for discharges of pollutants that meet certain regulatory requirements.

The facts presented in this case established that the city of San Francisco has a sewage system that when the system exceeds its capacity discharges pollutants; thus requiring a permit. In 2019, the Petitioner was issued a new NPDES permit for their Oceanside treatment plant. The Petitioner asserted that the EPA’s criteria for the new permit lacked precise definitions and quantifiable standards for the discharge of pollutants and explained that this ambiguity leads to challenges in compliance and enforcement.

The petition for writ of certiorari was filed on January 8, 2024, and granted on May 28, 2024.

The Petitioner argued the only permit conditions the EPA may impose under §1311 (b)(1)(C) of the Clean Water Act are those that fall within the Clean Water Act’s precise statutory definition of “effluent limitations” – not any other type of permit condition; however, the Court recognized that §1311 authorizes the EPA to impose limitations that do not fall within this definition[5].   The Supreme Court has previously recognized that water-quality prohibitions can supplement effluent limitations “so that numerous point sources, despite individual compliance with effluent limitations, may be further regulated to prevent water quality standards from falling below acceptable levels[6].”

The Court reasoned Congress used more extensive language, authorizing EPA to impose “any more stringent limitation, including those necessary to meet water quality standards” or “required to implement any applicable water quality standard[7].”  The Court further reasoned that the EPA exceeded its authority in imposing “end-result” requirements in NPDES permits and reaffirmed the Clean Water Act by emphasizing that the statute requires the EPA to specify clear, quantifiable effluent limitations in permits, rather than vague conditions tied to water quality outcomes.

In a joint statement by San Francisco City Attorney David Chiu and San Francisco Public Utilities Commission (SFPUC) General Manager Dennis Herrera, they indicated “[w]e are very pleased the Court issued the narrow decision San Francisco sought. This decision upholds the Clean Water Act’s critical role in protecting water quality and simply requires the EPA to fulfill its obligations under the Clean Water Act, as intended by Congress [8].”

The significance of this case is that it limits the scope of federal agency regulatory authority and shifts away from deferring to agency interpretation toward judicial review.  Although not mentioned in this case the Chevron doctrine is implicated. The Chevron doctrine’s long-standing precedent of deferring to a federal agency’s statutory interpretation in determining whether an agency has exceeded its authority was recently overturned on the grounds it conflicts with the Administrative Procedure Act [9]. Federal courts are encouraged to use their judgment in deciding a federal agency’s scope of authority.  

[1] City and County of San Francisco v. EPA, 601 U.S. 753 (2025). 

[2] Id. 

[3] 33 . §1251 et seq. 

[4] City and County of San Francisco v. EPA, 601 U.S. 753 (2025). 

[5] Id. 

[6] Id. 

[7] Id. 

[8] City and County of San Francisco (202, March 4).  SCOTUS issues decision in San Francisco’s favor in water quality permitting case [Press release].  SCOTUS issues decision in San Francisco’s favor in water quality permitting case – City Attorney of San Francisco

[9] Loper Bright Enterprises v Raimondo, 603 U.S. 369 (2024).