I. Introduction
On Tuesday, March 4, the United States Supreme Court issued a major decision limiting the scope of the Environmental Protection Agency’s (EPA) authority under the Clean Water Act (CWA) as relates to permits governing discharges by industry and municipalities into covered water bodies.
Specifically, the 5-4 ruling in City and County of San Francisco v. Environmental Protection Agency held that EPA cannot enforce permit provisions that “make a permittee responsible for the quality of the water in the body of water into which the permittee discharges pollutants.” No. 23-753, 2025 WL 676441, at *3 (U.S. Mar. 4, 2025). The Court ruled that under the CWA EPA cannot impose on discharging facilities the responsibility of achieving water quality results (“end-result” criteria) without providing specific direction on what permit holders can and cannot do, such as by imposing limits on each specific pollutant released by a facility. See id.
This decision may have immediate ramifications for EPA’s authority under the CWA to enforce end-result criteria in National Pollutant Discharge Elimination System (NPDES) permits as well as implications for businesses and municipalities that rely on them for CWA compliance.
II. Analysis of the Decision
a. Statutory Background
Under the CWA, EPA and authorized state agencies may issue permits that impose requirements on entities that wish to discharge “pollutants” into waters of the United States. See 33 U.S.C. § 1151 et seq. A cornerstone of the CWA’s regulatory structure is the NPDES permitting program. See EPA v. California ex rel. State Water Resources Control Bd., 426 U.S. 200, 205 (1976). These permits typically include “effluent limitations” on discharges that restrict the “quantities, rates, and concentrations of chemical, physical, biological, and other constituents.” 33 U.S.C. § 1362(11). NPDES permits also commonly set out other steps that a permittee must take, including testing, recordkeeping and reporting as well as requirements obligating a permittee to follow specified practices designed to reduce pollution. See 2025 WL 676441, at *3. Failure to comply with permit limitations exposes permittees to civil penalties and even criminal prosecution. See id. at *5 (citing 33 U.S.C. §§ 1319(c) and (d)). Under what is known as the “permit shield” provision, however, an entity that adheres to the terms of its permit is deemed to be compliant with the statute. See id. (citing 33 U.S.C. § 1342(k)).
This case involved a challenge to permit obligations known as “end-result” requirements or “receiving water limitations.” EPA imposed these end-result requirements under 33 U.S.C. § 1311(b)(1)(C). Rather than spell out the precise actions a permittee must take or refrain from taking, end-result permit requirements regulate by reference to the effect a polluting discharge will have on the quality of the waters that receive it. Id. at *3–4. Accordingly, these end-result permit provisions would effectively make a permittee responsible for the quality of the water into which the discharge occurs. Id. at *3.
b. Factual and Procedural Background
The city of San Francisco operates two combined treatment facilities: the Bayside facility, which discharges into San Francisco Bay, and the Oceanside facility, which empties into the Pacific Ocean. See City of San Francisco v. U.S. Envtl. Prot. Agency, 75 F.4th 1074, 1082 (9th Cir. 2023). The permit at issue in this case concerned only the Oceanside facility. Id. For many years, the Oceanside facility’s NPDES permit was renewed without controversy, but in 2019, the two end-result requirements that San Francisco challenged in this lawsuit were added. Id. at 1084–1085. The first of these prohibited the Oceanside facility from making any discharge that “contribute[s] to a violation of any applicable water quality standard” for receiving waters. Id. at 1085. The second provided that the city cannot perform any treatment or make any discharge that “create[s] pollution, contamination, or nuisance as defined by California Water Code section 13050.” Id. (internal quotation marks omitted).
All relevant state and federal agencies approved these two end-result requirements. San Francisco appealed to EPA’s Environmental Appeals Board (EAB), objecting to, among other things, the two new end-result provisions. See City and Cty. of San Francisco, 18 E.A.D. 322, 325 (2020). The EAB rejected San Francisco’s challenge, and the city then filed a petition for review in the Ninth Circuit under 33 U.S.C. § 1369(b)(1)(F). See 75 F.4th at 1088. A divided Ninth Circuit panel denied that petition, holding that § 1311(b)(1)(C) authorizes EPA to impose “any” limitations that seek to ensure that applicable water quality standards are satisfied in a receiving body of water. Id. at 1089–1090.
c. The Supreme Court Decision
The Supreme Court issued a 5-4 decision, written by Justice Samuel Alito, in favor of San Francisco, finding that the two challenged provisions of San Francisco’s NPDES permit “exceed EPA’s authority.” See 2025 WL 676441, at *3. In reaching this decision, the Court reasoned that the CWA’s text, the legislative history leading to the CWA and the CWA’s statutory scheme all demonstrate that EPA cannot regulate using end-result requirements.1
First, the Court looked to the text of § 1311(b)(1)(C), which requires a permit to contain, in addition to “effluent limitations,” “any more stringent limitation” that is “necessary to meet” certain “water quality standards” that are imposed under state law “or any other federal law or regulation”; and “any more stringent limitation” that is “required to implement any applicable water quality standard established pursuant to this chapter.” See 2025 WL 676441, at *7 (emphasis added by the Court). The Court stated that all the words highlighted in the prior sentence “suggest that the most natural reading of § 1311(b)(1)(C) is that it authorizes the EPA to set rules that a permittee must follow to achieve a desired result, namely, a certain degree of water quality.” See 2025 WL 676441, at *7.
Second, the Court examined the history of federal water pollution control. The Court noted that before 1972, the Water Pollution Control Act held permittees liable if the quality of the water into which they discharge pollutants failed to meet water quality standards. See id. at *8. However, when Congress overhauled that statute by passing the CWA, it chose not to regulate in the same way. Id. at *8–9. Congress instead imposed a regulatory scheme that sought to achieve “acceptable quality standards” by means of “direct restrictions” on polluters. See id. at *9 (citing EPA v. California, 426 U.S. at 204). Thus, according to the Court, EPA’s imposition of end-use requirements “would undo what Congress plainly sought to achieve when it scrapped the [Water Pollution Control Act’s] backward-looking approach.” Id.
Third, the Court reasoned that two features of the broader statutory scheme of the CWA also militate against the validity of end-use requirements: (1) the statute’s “permit shield” and (2) the statute’s lack of a mechanism for fairly allocating responsibility among multiple dischargers contributing to water quality violations. The permit shield provision, 33 U.S.C. § 1342(k), deems a permittee to be in compliance with the CWA as long as it follows all the terms in its permit. This protection is “very valuable because violations of the CWA, even if entirely inadvertent, are subject to hefty penalties.” Id. The Court reasoned that this valuable protection would be “eviscerated if the EPA could impose a permit provision making the permittee responsible for any drop in water quality below the accepted standard” regardless of whether the permittee complies with all other concrete provisions in its NPDES permit. Id. at *10.
Next, the Court pointed to the absence of any provision in the CWA dealing with the “problem that arises when more than one permittee discharges into a body of water with substandard water quality.” Id. The Court explained that it is hard to accept the idea that Congress contemplated the enforcement of end-use requirements when it did not provide any method for dealing with multi-discharger situations—a common occurrence, since “dozens or even hundreds of … permitted and unpermitted discharges” flow into the same water body. Id. (citation and internal quotes omitted).
Finally, the Court relied on two policy arguments for its holding: (1) businesses and municipalities would not be harmed by the elimination of end-use requirements, and (2) the “EPA possesses the expertise … and the resources necessary to determine what a permittee should do.” Id. at *11. In other words, the Court determined that EPA should use its own resources to determine how to protect water quality rather than leave businesses and cities to figure out how to do so.
III. Conclusion: Possible Impact
San Fransisco’s position was supported by the U.S. Chamber of Commerce and multiple trade associations, in large part because of the vague, uncertain and burdensome nature of end-use requirements. This decision will require EPA to issue more concrete requirements in its NPDES permits, which should provide industry and municipalities with greater certainty about what they will need to do to comply with those permits. Such certainty will likely lead to decreased compliance risk and a greater sense of preparedness on the part of a city or business when a facility is reviewed by EPA to ensure CWA compliance.
Moreover, this decision places responsibility for figuring out how to maintain overall water quality on the regulators. This should result in cost savings for businesses and municipalities, which will no longer be required to invest resources in determining how discharge levels interact with overall water quality.
But the decision also poses potential challenges, as it could lead to increased delays or denials of NPDES permits. As Justice Amy Coney Barrett noted in her dissent, EPA often lacks the requisite information to issue an NPDES permit prescribing the specific effluent limitations a business or city can discharge. See id. at 18. Because that information can often take a very long time to gather, EPA often issues NPDES permits with end-use requirements to avoid lengthy delays or denials that could slow business projects and municipal developments. See id. at *17–18. In the words of Justice Barrett, it might be “preferable for EPA to impose broadly worded conditions in its permits than to deny permits altogether and potentially shut down San Francisco’s sewer system.” Id. at *18.
WilmerHale’s Energy, Environment and Natural Resources team will continue to closely follow the impact of this Supreme Court decision.
