Permit Shields and Power Shifts: What San Francisco v. EPA Means for Water Law

On March 4, 2025, in a 5-4 decision, the Supreme Court of the United States (the “Court”) held that the EPA cannot impose end-result requirements when issuing National Pollutant Discharge Elimination System (“NPDES”) permits. The decision, City and County of San Francisco, California v. Environmental Protection Agency 145 S. Ct. 704 (2025), represents a significant limitation on the EPA’s authority under the Clean Water Act (“CWA”).

Background of Case

This case deals with the EPA’s addition of “end-result requirements” to NPDES permits for the City of San Francisco (the “City”). An NPDES permit is a permit issued by EPA or an authorized state under § 402 of the CWA for the discharge of pollutants into “waters of the United States.” The City operates a combined sewer system that collects both sewage and stormwater runoff. During heavy rains, the sewer system can exceed its capacity, resulting in sewer overflows that would discharge pollutants into the Pacific Ocean. Because of this, for many years, the City would apply for and receive NPDES permits from the EPA for its discharge from the sewer system.

In 2019, the EPA added two end-result requirements to the City’s NPDES permit: (1) the City could not discharge in any way that would contribute to a violation of any applicable water quality standard in a receiving water; and (2) the City could not perform treatment or make a discharge that creates pollution, contamination, or nuisance. The City brought a legal action against the EPA over these additional requirements, arguing that the EPA had overreached its authority granted by Congress by imposing overly broad limitations. The EPA, in turn, argued that it was operating under authority granted to it under CWA § 301(b)(1)(C), 33 U.S.C. § 1311(b)(1)(C).

Court’s Ruling

The Court ultimately agreed with the City, holding that the EPA does not have the authority under CWA § 1311(b)(1)(C) to impose end-result requirements in NPDES permits. Initially, however, the Court rejected the City’s argument that NPDES permits could include only technology-based or water quality-based effluent limitations adopted pursuant to 33 U.S.C. § 1311. The Court concluded that the statutory language authorized imposition of other types of NPDES permit conditions that do not qualify as effluent limitations (e.g., monitoring requirements, or requirements to implement best management practices such as are often found in NPDES general permits for the discharge of stormwater).  

Despite rejecting the City’s initial argument, the Court agreed with the City’s narrower argument that the CWA does not authorize imposition of end-result requirements that create the potential for non-compliance based on conditions in a receiving water. The Court reasoned that the CWA authorizes the EPA to impose specific limitations on a permittee’s actions and the quality of its discharges, but that the agency’s authority does not extend to imposing a condition that “simply tells a permittee that a particular end result must be achieved and that it is up to the permittee to figure out what it should do.” In short, the EPA must lay out specific steps and limitations for NPDES permit holders; it cannot simply require permit holders to achieve a vague goal without laying out the steps to achieve that goal.

Further, the Court held that allowing end-result requirements would undercut the CWA’s permit shield, which protects permit holders from enforcement actions as long as they abide by the terms of their discharge permit. (See 33 U.S.C. § 1342(k).) The Court reasoned that allowing end-result requirements would put permit holders at risk of potential “harsh” or “crushing” civil penalties if they were unable to meet these requirements, and that the requirements might be impossible to meet in some cases even if a permittee is strenuously attempting to comply with its permit (e.g., in a case where there are multiple dischargers to a poor quality water). The Court concluded that allowing broad end-result requirements was inconsistent with the CWA’s permit shield provision.

Among many other positions, EPA argued that precluding end-result requirements could limit the ability of permitting agencies to issue, or delay the issuance of, general NPDES permits, such as stormwater discharge permits for construction and for industrial activities.  Historically, these permits often contained end-result requirements (e.g., a condition forbidding discharges from causing or contributing to violations of surface water quality standards in receiving waters). The Court was not swayed by this argument, noting that such permits could still be issued with conditions addressing operational requirements and best management practices. 

What This Means for the EPA and NPDES Permit Holders

San Francisco v. EPA marks a significant limitation on the EPA’s authority under the CWA. Going forward, the EPA must ensure that its permit requirements are specific and measurable to ensure enforceability. Although environmental advocates are concerned that this will have a negative impact on water protections, NPDES permit holders may find it easier to manage and achieve compliance with new requirements and clearer standards. However, it remains to be seen whether and to what extent federal and state permitting authorities modify effluent limitations in individual NPDES permits if such permits no longer may include end-result requirements.  Likewise, it is unclear how general NPDES permits will be modified if they no longer are authorized to include end-result requirements.