Clean Water Act Compliance Post-San Francisco v. EPA

Timothy Cohn

Earlier this month the Supreme Court rendered invalid the National Pollution Discharge Elimination System (“NPDES”) permit authorizing the City and County of San Francisco’s wastewater treatment facility to operate, and to discharge treated wastewater into the Pacific Ocean.[1] In its holding, the Court found certain portions of the permit deficient under Section 1311(b)(1)(C) of the Clean Water Act (“CWA”), finding that the statute does not support the use of narrative standards.[2]

This decision resolves a long-standing dispute about the use of narrative standards in NPDES permitting and is expected to provide greater clarity for permitted entities seeking to comply with permit conditions.

The Case

San Francisco operates and maintains combined wastewater and stormwater treatment plants which operate pursuant to a NPDES permit.[3] One such plant, the Oceanside facility, empties treated water into the Pacific Ocean.[4] During severe weather events, this system tends to overflow, spilling untreated wastewater and stormwater into the ocean.[5]

To remedy this issue, EPA negotiated two permit conditions aimed at ensuring compliance with CWA Water Quality Standards (“WQS”) – a standard which state and local governments must meet under 33 U.S.C. §1251.[6] The first condition prohibits the facility from making any discharge that “contribute[s] to a violation of any applicable water quality standard” for the receiving water body.[7] The second provision prohibited the City from engaging in conduct which “create[s] pollution, contamination, or nuisance as defined by California Water Code §13050.”

San Francisco sued the EPA, claiming that these provisions were tantamount to an “end-result” provision which inappropriately shifted the burden of meeting applicable WQS from the state to the permitted entities, outside the scope of the statute.[8]

The majority concluded that an “end-result” approach to CWA permitting was inconsistent with 33 U.S.C. §1342(k) – the CWA’s “permit shield” provision which leaves a party in compliance with a permit’s specific terms protected from liability.[9] Further, the Court concluded that conditioning a permit upon compliance with WQS violated the statute because of “the problem that arises when more than one permittee discharges into a body of water with substandard water quality.”[10]

Implications for Permitted Entities

It is widely expected that the Supreme Court’s holding in City and County of San Francisco v. EPA will require the EPA to issue more specific permits with more listed specifications and restrictions.[11] Business entities, utility companies, and other regulated entities will be better positioned to be in compliance with the statute’s mandates as each permit will be more detailed and thorough in its requirements.[12]

In turn, this will have the effect of broadening the CWA’s permit shield provision to a greater number of regulated entities—something which environmental advocates criticize as weakening the CWA’s enforcement power.[13]

While it is clear that the EPA and Department of Justice have fewer avenues to enforce the CWA without being able to rely upon narrative standards or WQS in permit conditions, this decision will have the benefit of clarifying due process concerns articulated by San Francisco[14] and various amicus parties.[15]

Conclusion

Going forward, the main takeaway for all regulated entities is that the compliance landscape just became more straightforward.[16] Both public and private regulated entities will benefit from having additional notice of permit terms and conditions, and there is greater predictability and fair notice of what conduct is permissible, and which is illegal. This will likely result in the additional benefit of lessening the exposure of such entities to costly civil monetary penalties under the CWA.[17]

Permit officers will play an important role next time each entity’s permit is up for renegotiation and renewal as they may be able to argue for greater specificity and granularity to guide operations and avoid running afoul of the law.

[1] City and County of San Francisco v. EPA, No. 23-753, slip op. (U.S. Mar. 4, 2025).

[2] Id. at 3–4.

[3] Id. at 11-12.

[4] Id.

[5] Id.

[6] San Francisco Pub.Utilities Comm’n, Supreme Court Issues Decision in San Francisco’s Favor in Water Quality Permitting Case, (Mar. 4, 2025), https://www.sfpuc.gov/about-us/news/supreme-court-issues-decision-san-franciscos-favor-water-quality-permitting-case.

[7] San Francisco, No. 23-753, slip op. at 11.

[8] Reply Brief for Petitioners at 5, City and County of San Francisco v. EPA, No. 23-753 (U.S. Apr. 30, 2024) (“[C]onditions that simply direct permitholders not to cause or contribute to water quality standards violations—like the Generic Prohibitions—'effectively ignore’ the line Congress drew ‘by making the ultimate, overall “water quality standards” themselves the applicable [effluent] “limitation” for an individual discharger.’”).

[9] Id. at 10.

[10] Id. at 20.

[11] City and County of San Francisco v. EPA: Implications for Clean Water Act Permittees, Nossaman LLP (Mar. 6, 2024), https://www.nossaman.com/newsroom-insights-city-and-county-of-san-francisco-vs-epa-implications-for-clean-water-act-permittees.

[12] Id.

[13] American Rivers, American Rivers Statement on San Francisco v. EPA Supreme Court Decision Weakening Clean Water Act Enforcement, (Mar 5. 2025), https://www.americanrivers.org/media-item/american-rivers-statement-on-san-francisco-v-epa-supreme-court-decision-weakening-clean-water-act-enforcement/.

[14] Reply Brief for Petitioner at 19, City & Cnty. of San Francisco v. EPA, No. 23-753 (U.S. filed Sept. 25, 2024) (“Permit terms like the Generic Prohibitions undermine the finality the permit shield guarantees by exposing permitholders to enforcement actions without fair notice.”) (citing 33 U.S.C. § 1342(k)).

[15] See e.g., Brief Amici Curiae of National Mining Association, et al., in Support of Petitioner, City and County of San Francisco v. Environmental Protection Agency, No. 23-753 (U.S. filed Feb. 12, 2024).

[16] See supra n. 11–12 (“The opinion now shifts the responsibility for developing explicit compliance measures onto EPA in crafting NPDES permit requirements rather than allowing the agency to rely on general language for ensuring water quality that previously placed the burden onto permittees.”).

[17] See 40 C.F.R. § 19.4 (2020).