City and County of San Francisco v. Environmental Protection Agency Brings Questions of Agency Deference Back in Front of the Supreme Court
October 3, 2024 by Berit DeGrandpre

The Golden Gate Bridge with a view of San Francisco in the background.
The Supreme Court will hear a challenge to a pollution discharge permit issued by EPA under the Clean Water Act. The case raises questions of statutory interpretation, administrative, and environmental law that have been hot topics at the Supreme Court in recent terms.
The Environmental Protection Agency (“EPA”) is back in front of the Supreme Court this term defending against the City and County of San Francisco’s (“San Francisco”) challenge to a pollution discharge permit issued by the Agency under authority granted to it in the Clean Water Act (“CWA”).[1] This case comes on the heels of the Court’s decision last term to overrule the decades long precedent, Chevron, which granted judicial deference to agency interpretation of statutes.[2] At the nexus of hot topics for the Court: statutory interpretation, administrative and environmental law, City and County of San Francisco v. Environmental Protection Agency may illustrate how the Court expects agency deference – or lack thereof – to operate in a post-Chevron landscape.[3]
In 2019, EPA approved San Francisco’s National Pollutant Discharge Elimination System (“NPDES”) permit (“Permit”), for the City’s Oceanside combined sewer system and wastewater treatment facility.[4] The City seeks judicial review of requirements within the permit, arguing that EPA exceeded the authority granted to it by the CWA.[5] Specifically, San Francisco challenges the narrative prohibition section of the permit, which provides that “[d]ischarge shall not cause or contribute to a violation of any applicable water quality standard.”[6] San Francisco contends that this requirement is problematic because it is inconsistent with the statutory scheme of the CWA,[7] which empowers EPA to impose specific limitations on discharged pollutants but not to hold individual permitholders responsible for overall quality of the water into which pollutants are discharged.[8]
The Ninth Circuit disagreed with San Francisco, upholding the narrative prohibitions in the Permit.[9] It found the CWA gives EPA “broad authority to impose limitations necessary to ensure the discharger’s adherence” to relevant water quality standards, and that the agency acted consistently with the Act’s directive.[10] The Ninth Circuit was persuaded in particular by the combination of the general narrative provision “along with numeric effluent limitations,”[11] such that the narrative provision acted not as a target, but a “backstop” to protect ocean water quality should the effluent limitations be insufficient to ensure compliance with the CWA.[12] Notably, the Ninth Circuit reviewed the challenge with deference to the agency’s interpretation of the statute.[13] EPA is unlikely to receive the same level of deference at the Supreme Court.[14] However, it is unclear if this will prove fatal for the Agency.
In Loper Bright Enterprises v. Raimondo, Chief Justice Roberts wrote in overruling Chevron that the Administrative Procedure Act, which establishes the governing rules for all agencies, “prescribes no deferential standard for courts to employ,” when evaluating agency interpretations of law.[15] Thus, courts should “set aside any such action inconsistent with the law as they interpret it.”[16] After Loper Bright, it is clear that if the Court disagrees with an agency’s interpretation, or concludes that an alternative interpretation is more correct, the reviewing court owes no deference to the agency’s interpretation.[17] Still, the Court may pay some, albeit limited, consideration to an agency’s interpretation. Consideration of an agency’s interpretation depends on an agency’s expertise, thoroughness of consideration, validity of reasoning, and consistency with other pronouncements, including “all those factors which give it power to persuade, if lacking power to control.”[18]
It is unclear what this will spell for EPA. As both EPA and the Ninth Circuit have carefully pointed out, the same or similar narrative prohibitions are found in NPDES permits across the country.[19] Thus, for the past three decades, the Agency has acted consistently in this regard.[20] Additionally, determining effluent limitations for individual dischargers draws heavily on the Agency’s expertise. Still though, the narrative prohibitions at issue arguably do not draw significantly on the Agency’s expertise and provide only some instruction on which “litigants could properly resort for guidance.”[21] Ultimately, the question will be decided by the Court’s textual determination of the CWA’s plain meaning, which will control. If the Court determines that EPA’s interpretation “is not the best, it is not permissible.”[22] Whatever the outcome, the case may prove instructive for lower courts and litigants looking for interpretive guidance in a post-Loper Bright landscape.
[1] City and Cnty. of S.F. v. Env’t. Prot. Agency, 144 S. Ct. 2578 (2024) (arguments are scheduled for October 16, 2024).
[2] See Loper Bright Enters. v. Raimondo, 144 S. Ct. 2244, 2273 (2024) (overruling Chevron, U.S.A., Inc. v. Nat. Res. Def. Council, Inc., 104 S. Ct. 2778 (1984)).
[3] City and Cnty. of S.F. v. Env’t. Prot. Agency, 144 S. Ct. 2578 (2024).
[4] City and Cnty. of S.F. v. Env’t. Prot. Agency, 75 F.4th 1074, 1088 (9th Cir. 2023). Pursuant to the CWA, a polluter needs a permit (San Francisco is required to obtain both federal and state level permits) to discharge a pollutant into a navigable water source. Brief for Petitioner at 3, City and Cnty. of S.F. v. Env’t. Prot. Agency, 144 S. Ct. 2578 (2024) (No. 23-753). The Act requires polluters to obtain National Pollutant Discharge Elimination System (“NPDES”) permits that set “effluent limitations.” 33 U.S.C. § 3111 (Section 301). Effluent limitations impose “direct restrictions on discharges” and specify restrictions with which a permitholder’s discharge must conform. Id.; see also Brief for Petitioner at 3, City and Cnty. of S.F. v. Env’t. Prot. Agency, 144 S. Ct. 2578 (2024) (No. 23-753).
[5] Id. (discussing EPA’s Environmental Appeals Board’s decision to deny San Francisco’s petition for review of the Permit. This denial prompted the City to seek judicial review. See City and Cnty. of S.F., 18 E.A.D. 322 (EAB 2020)).
[6] City and Cnty. of S.F. v. Env’t. Prot. Agency, 75 F.4th 1074, 1085 (9th Cir. 2023) (discussing 2019 NPDES Oceanside permit Section V and Attachment G; Section I.I.1).
[7] The provision of the CWA at issue here, “Effluent Limitations,” 33 U.S.C. § 1311(b)(1)(C) reads in relevant part, “In order to carry out the objective of this chapter there shall be achieved – any more stringent limitation, including those necessary to meet water quality standards, treatment of standards, or schedules of compliance, established pursuant to any State law or regulations. . . or any other Federal law or regulation, or required to implement any applicable water quality standard established pursuant to this chapter.”
[8] Brief for Petitioner 2-4, City and Cnty. of S.F. v. Env’t. Prot. Agency, 144 S. Ct. 2578 (2024) (No. 23-753).
[9] City and Cnty. of S.F. v. Env’t. Prot. Agency, 75 F.4th 1074 (9th Cir. 2023).
[10] Id. at 1089 (citing 33 U.S.C. § 1311(b)(1)(C)).
[11] City and Cnty. of S.F. v. Env’t. Prot. Agency, 75 F.4th 1074, 1091 (9th Cir. 2023) (emphasis added).
[12] Id.
[13] Id. at 1089 (“Under the APA, we must set aside an agency’s decision if it is ‘arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law.’ 5 U.S.C. § 706(2)(A). This standard of review is ‘highly deferential.’ Kern Cnty. Farm Bureau v. Allen, 450 F.3d 1072, 1076 (9th Cir. 2006).”).
[14] Loper Bright Enters. v. Raimondo, 144 S. Ct. 2244, 2267 (2024) (“interpretive issues arising in connection with a regulatory scheme often ‘may fall more naturally into a judge’s bailiwick’ than an agency’s.”) (citing Kisor v. Wilkie, 139 U.S. 558, 578 (2019)).
[15] Id. at 2261.
[16] Id.
[17] Id. at 2295 (Kagan, J., dissenting) (“[T]he majority today gives itself exclusive power over every open issue – no matter how expertise-driven or policy-laden – involving the meaning of regulatory law. As if it did not have enough on its plate, the majority turns itself into the country’s administrative czar. It defends that move as one (suddenly) required by the (nearly 80-year-old) Administrative Procedure Act. But the Act makes no such demand.”).
[18] Id. at 2267 (citing Skidmore v. Swift & Co., 65 S. Ct. 161, 164 (1944)).
[19] City and Cnty. of S.F. v. Env’t. Prot. Agency, 75 F.4th 1074, 1090 (9th Cir. 2023).
[20] Id.
[21] Loper Bright Enters. v. Raimondo, 144 S. Ct. 2244, 2259 (2024) (citing Skidmore v. Swift & Co., 65 S. Ct. 161, 164 (1944)).
[22] Id. at 2266.