FOR PUBLICATION

UNITED STATES COURT OF APPEALS

FOR THE NINTH CIRCUIT

CITY AND COUNTY OF SAN 

FRANCISCO, 

Petitioner, 

 v. 

U.S. ENVIRONMENTAL 

PROTECTION AGENCY, 

Respondent.

No. 21-70282 

Environmental 

Protection Agency

OPINION

On Petition for Review of an Order of the

Environmental Protection Agency

Argued and Submitted March 17, 2022

San Francisco, California

Filed July 31, 2023

Before: William A. Fletcher, Ronald M. Gould, and Daniel 

P. Collins, Circuit Judges.

Opinion by Judge W. Fletcher;

Dissent by Judge Collins
2 CITY & COUNTY OF SAN FRANCISCO V. USEPA

SUMMARY*

National Pollutant Discharge Elimination System 

Permits

The panel denied the City and County of San Francisco’s 

petition for review of a final order of the U.S. Environmental 

Protection Agency (“EPA”) denying review of San 

Francisco’s federal National Pollutant Discharge 

Elimination System (“NPDES”) permit for its Oceanside 

combined sewer system and wastewater treatment facility.

The NPDES permit, which was issued pursuant to the 

Clean Water Act of 1972 (“CWA”), 33 U.S.C. §§ 1251–

1387, allows San Francisco to discharge from its wastewater 

system into the Pacific Ocean, and includes (1) two general 

narrative prohibitions on discharges that cause or contribute 

to violations of applicable water quality standards, and (2) a 

requirement that San Francisco update its long-term control 

plan for its combined sewer overflows. 

The panel held that the EPA had authority under the 

CWA to include the two general narrative prohibitions. 

Noting that Supreme Court precedent, this Circuit’s prior 

cases, and prior Environmental Appeals Board decisions 

support the legality and confirm the enforceability of general 

narrative prohibitions in permits issued under the CWA, the 

panel held that the two narrative provisions were consistent 

with the CWA and its implementing regulations. The panel 

further held that the EPA was not required to follow the 

procedures set forth in 40 C.F.R. § 122.44(d)(1)(i)-(vii) for 

* This summary constitutes no part of the opinion of the court. It has 

been prepared by court staff for the convenience of the reader.
CITY & COUNTY OF SAN FRANCISCO V. USEPA 3

deriving pollutant-specific effluent limitations in imposing 

the general narrative provisions, and that the EPA’s decision 

to impose the general narrative provisions was rationally 

connected to evidence in the record indicating that a 

“backstop” to the more specific provisions would be useful 

in protecting beneficial uses.

The panel next held that the EPA had authority under its 

Combined Sewer Overflow Control Policy to require San 

Francisco to update its long-term control plan for its 

combined sewer overflows and reevaluate alternatives for its 

combined sewer overflow discharges to sensitive areas. The 

EPA’s ability to require San Francisco to update its longterm control plan was not conditioned on a finding that water 

quality standards were not being met and was rationally 

supported by evidence in the record.

Dissenting, Judge Collins would grant San Francisco’s 

petition for review, vacate the challenged permit conditions, 

and remand the case to the agency for further 

consideration. First, the two general narrative limitations 

were inconsistent with the text of the CWA, and, by 

including them, the EPA fundamentally abdicated the 

regulatory task assigned to it under the CWA. Second, 

because no determination was made that San Francisco’s 

Oceanside System had caused the violation of any applicable 

water control standards, the EPA lacked authority under the 

Combined Sewer Overflow Control Policy to impose a 

condition requiring San Francisco to submit a revised longterm control plan.
4 CITY & COUNTY OF SAN FRANCISCO V. USEPA

COUNSEL

Andrew C. Silton (argued) and Richard S. Davis, Beveridge 

& Diamond PC, Washington, D.C.; Estie M. Kus and John 

Roddy, Deputy City Attorneys; Sheryl L. Bregman, Utilities 

General Counsel; Yvonne R. Meré, Chief Deputy City 

Attorney; David Chiu, City Attorney; San Francisco City 

Attorney’s Office; City and County of San Francisco; San 

Francisco, California; for Petitioner.

Elisabeth Carter (argued), Attorney; Todd Kim, Assistant 

Attorney General; Environment and Natural Resources 

Division, United States Department of Justice; Washington, 

D.C.; Peter Z. Ford, Pooja Parikh, and Marcela Von Vacano, 

Attorneys; United States Environmental Protection Agency; 

Washington, D.C.; for Respondent.

David Chung and Elizabeth B. Dawson, Crowell & Moring 

LLP, Washington, D.C.; Hilary Meltzer, Assistant 

Corporation Counsel; Georgia M. Pestana, Corporation 

Counsel of the City of New York; New York City Law 

Department; New York, New York; Roberta L. Larson, 

Somach Simmons & Dunn, Sacramento, California; for 

Amici Curiae National Association of Clean Water 

Agencies, California Association of Sanitation Agencies, 

Louisville/ Jefferson County Metropolitan Sewer District, 

and City of New York.

Marc N. Melnick and Daniel S. Harris, Deputy Attorneys 

General; Annadel A. Almendras and Myung J. Park, 

Supervising Deputy Attorneys General; Robert W. Byrne, 

Senior Assistant Attorney General; Office of the California 

Attorney General; Oakland, California; for Amicus Curiae 

California Regional Water Quality Control Board, San 

Francisco Bay Region. 
 CITY & COUNTY OF SAN FRANCISCO V. USEPA 5 

James N. Saul, Earthrise Law Center at Lewis & Clark Law 

School, Portland, Oregon, for Amici Curiae Law Professors.

OPINION

W. FLETCHER, Circuit Judge: 

The City and County of San Francisco (“San Francisco”) 

petitions for review of a final order of the U.S. 

Environmental Protection Agency (“EPA”) denying review 

of San Francisco’s federal National Pollutant Discharge 

Elimination System (“NPDES”) permit for its Oceanside 

combined sewer system and wastewater treatment facility

(“wastewater system”). This NPDES permit, issued 

pursuant to the Clean Water Act of 1972 (“CWA”), 33 

U.S.C. §§ 1251–1387, allows San Francisco to discharge 

from its wastewater system into the Pacific Ocean. San 

Francisco contends that EPA acted arbitrarily and 

capriciously, and contrary to the CWA, by including in the 

final permit: (1) two general narrative prohibitions on 

discharges that cause or contribute to violations of applicable 

standards for water quality, and (2) a requirement that San 

Francisco update its long-term control plan (“LTCP”) for its 

combined sewer overflows (“CSOs”). We hold that the 

CWA authorizes EPA to include in the Oceanside NPDES 

permit the challenged provisions, and that EPA’s decision to 

do so was rationally connected to evidence in the 

administrative record. We therefore deny San Francisco’s 

petition for review. 
6 CITY & COUNTY OF SAN FRANCISCO V. USEPA

We use a number of acronyms and short-form references 

in this opinion. For the convenience of the reader, we list 

them here.

Acronyms:

• APA: Administrative Procedure Act

• CSD: Combined sewer discharge

• CSO: Combined sewer overflow

• CWA: Clean Water Act

• EAB: Environmental Appeals Board

• EPA: Environmental Protection Agency

• LTCP: Long-term control plan

• NPDES: National Pollutant Discharge Elimination 

System

• NRDC: Natural Resources Defense Council

• WQBEL: Water quality-based effluent limitation

• WQS: Water quality standards

Short-form references:

• 1979 Ocean Plan Exception: California State Water 

Board Order No. 79-16

• Basin Plan: Water Quality Control Plan for the San 

Francisco Bay Basin

• CSO Control Policy or Policy: Combined Sewer 

Overflow Control Policy

• CSO Guidance: Combined Sewer Overflows: Guidance 

for Permit Writers

• LTCP Synthesis: San Francisco Wastewater Long Term 

Control Plan Synthesis

• Ocean Plan: Water Quality Control Plan for Ocean 

Waters of California

• Regional Water Board: California Regional Water 

Quality Control Board for the San Francisco Bay Region
CITY & COUNTY OF SAN FRANCISCO V. USEPA 7

• Strategy: National Combined Sewer Overflow Control 

Strategy

• Wastewater system: combined sewer system and 

wastewater treatment facility

I. Background

A. Regulation of Combined Sewer Systems

Most cities in the United States, including San Francisco, 

operate combined sewer systems. See National Combined 

Sewer Overflow Control Strategy, 54 Fed. Reg. 37370, 

38371 (Sept. 8, 1989). Combined sewer systems are 

wastewater collection systems that convey both sewage and 

storm water to a treatment plant through a single set of pipes. 

40 C.F.R. § 122.2. During heavy rain or snow, combined 

sewer overflows (“CSOs”) can occur when water in the 

system exceeds the capacity of the pipes or the treatment 

plant, leading to discharges of pollutants into surface waters. 

Combined Sewer Overflow (CSO) Control Policy, 59 Fed. 

Reg. 18688, 18689 (Apr. 19, 1994). CSOs are “mixtures of 

domestic sewage, industrial and commercial wastewaters, 

and storm water runoff.” Id. They “often contain high levels 

of suspended solids, pathogenic microorganisms, toxic 

pollutants, floatables, . . . and other pollutants.” Id.

Under the CWA, an NPDES permit is required for the 

discharge of “any pollutant by any person” from any “point 

source” into the navigable waters of the United States. 33 

U.S.C. §§ 1311(a)–(b), 1342(a); 40 C.F.R. § 122.1(b)(1). 

Municipal CSOs are discharges from “point sources” under 

the CWA and therefore require NPDES permits. National 

Combined Sewer Overflow Control Strategy, 54 Fed. Reg. 

at 37371; see also 33 U.S.C § 1342(q) (identifying CSOs as 

discharges subject to the NPDES permitting requirements). 
8 CITY & COUNTY OF SAN FRANCISCO V. USEPA

1. NPDES Permitting System

NPDES permits are issued by both EPA and state 

authorities. Under the CWA, EPA may authorize States to 

issue NPDES permits for discharges into waters within the 

State’s jurisdiction. 33 U.S.C. § 1342(b)–(c). However, 

EPA retains authority to issue permits for discharges into 

ocean waters more than three miles from the shore. See id. 

§ 1362(8) (defining the State’s territorial seas as extending 

three miles from the coast). When both state and federal 

permits are needed for a particular treatment facility, the 

permitting processes may be consolidated, and permits may 

be issued jointly or separately. 40 C.F.R. § 124.4(c). 

To issue an NPDES permit for discharges into ocean 

waters, state and federal authorities must establish that the 

discharge will satisfy (1) water quality standards; (2) effluent 

limitations—i.e., restrictions on how much pollutant any 

point source may discharge; and (3) antidegradation criteria. 

33 U.S.C. § 1342(a), 1343; see also id. §§ 1311 (effluent 

limitations), 1313 (water quality standards and 

implementation plans), 1312 (water-quality related effluent 

limitations), 1317 (effluent limitations for toxic pollutants); 

40 C.F.R. § 122.44. NPDES permits also include 

monitoring and reporting requirements, compliance 

schedules, and management practices. See, e.g., 40 C.F.R. 

§§ 122.41, 122.44. 

Water quality standards (“WQS”) specify (1) a body of 

water’s “designated use” (e.g., recreation, water supply, or 

propagation of fish) and (2) “water quality criteria” (i.e., 

numeric or narrative benchmarks to protect a designated 

use). Id. §§ 130.2(d), 131.3(b), 131.10(a). State-defined 

WQS are used as the basis for specific effluent limitations in 

NPDES permits. 33 U.S.C. §§ 1311(b)(1)(C), 1370; 40 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 9

C.F.R. §§ 122.4(d), 122.44(d)(1), 131.4(a). EPA reviews 

state-adopted WQS and is authorized to approve or 

disapprove them in accordance with the CWA’s 

requirements. 40 C.F.R. § 131.5(a). 

Effluent limitations are defined as “any restriction 

imposed . . . on quantities, discharge rates, and 

concentrations of pollutants which are discharged from point 

sources into waters of the United States.” Id. § 122.2 

(internal quotation marks omitted). Effluent limitations are 

typically expressed numerically, in the maximum mass of a 

pollutant that may be discharged. See id. § 122.45(f). 

Technology-based effluent limitations establish discharge 

standards based on levels of effluent quality achievable by 

certain pollution treatment technologies for different 

categories of pollutants. Id. §§ 122.44(a)(1), 125.3(a). 

Water quality-based effluent limitations (“WQBELs”) 

establish more stringent discharge requirements when 

necessary to meet applicable WQS. 33 U.S.C.

§ 1311(b)(1)(C); 40 C.F.R. § 122.44(d). Permitting 

agencies may impose “best management practices,” or 

specific operational requirements or prohibitions, rather than 

numeric limitations, if numeric effluent limitations are not 

feasible. 40 C.F.R. §§ 122.2, 122.44(k)(3). 

2. NPDES Permits for CSOs

In 1989, EPA issued the National Combined Sewer 

Overflow Control Strategy (“the Strategy”), which sets forth 

its NPDES permitting strategy to control CSOs. By 

addressing discharges from combined sewer systems, the 

Strategy “complement[ed]” the preexisting regulatory 

control programs for sanitary sewer systems and separate 

storm sewer systems. National Combined Sewer Overflow 

Control Strategy, 54 Fed. Reg. at 37371. Recognizing that 
10 CITY & COUNTY OF SAN FRANCISCO V. USEPA

CSOs “have been shown to have severe adverse impacts on 

water quality, aquatic biota, and human health,” EPA sought 

to establish a uniform nationwide permitting approach to 

control these discharges. Id. The Strategy provided that 

under the CWA, “[a]ll CSO discharges must be brought into 

compliance with technology-based requirements and State 

water quality-based requirements” using “a combination of 

CSO control measures.” Id. According to the Strategy, a 

municipality’s publicly owned treatment works (water 

treatment plant) “is responsible for planning and 

coordinating a system-wide approach” to CSO control. Id. 

at 37372. The Strategy specified that CSO point sources 

“discharging without a permit are unlawful and must be 

permitted or eliminated.” Id. at 37371. 

In 1994, EPA issued the Combined Sewer Overflow 

Control Policy (“CSO Control Policy” or “Policy”) as part 

of its national strategy for CSO control. Combined Sewer 

Overflow Control Policy, 59 Fed. Reg. at 18688–89. In 

2000, Congress made the CSO Control Policy legally 

binding when it enacted the Wet Weather Water Quality Act. 

Pub. L. No. 106-554, § 112, 114 Stat. 2763, 2763A-224 to 

2763A-225 (2000) (codified at 33 U.S.C. § 1342(q)(1)). The 

CSO Control Policy prohibits all CSOs that occur in dry 

weather. Combined Sewer Overflow Control Policy, 59 

Fed. Reg. at 18689. The Policy requires municipalities with 

combined sewer systems to implement extensive control 

measures (the “Nine Minimum Controls”) and to develop 

and implement a Long-Term Control Plan (“LTCP”) to 

protect water quality during wet weather. Id. at 18691. 

Under the CSO Control Policy, required minimum 

control measures include elimination of all dry-weather 

CSOs, control of all “solid and floatable materials in CSOs,” 

maximization of storage and flow to the treatment plant 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 11

during wet-weather events, public notification of CSO 

occurrences, and ongoing monitoring of CSOs and efficacy 

of the control measures. Id. A municipality’s LTCP must 

address the following “minimum elements”: (1) 

characterization, modeling, and monitoring of the combined 

sewer system and CSOs, including evaluation of rainfall 

records; (2) a process for public participation in LTCP 

development; (3) special prioritization of control of CSOs 

into “sensitive areas,” such as waters used for drinking or 

recreation; (4) evaluation of alternative control measures to 

achieve different benchmarks, such as zero versus one to 

three CSOs per year; (5) “cost/performance” analysis of the 

control measure alternatives; (6) an operational plan to 

implement the selected CSO controls; (7) a plan to maximize 

wet-weather water treatment capacity at existing treatment 

plants; (8) an implementation schedule, including 

construction phasing; and (9) a post-construction 

compliance monitoring program. Id. at 18691–94. 

A municipality’s LTCP must adopt one of two 

approaches to demonstrate that its control program satisfies 

the requirements of the CWA: a “Presumption Approach” or 

a “Demonstration Approach.” Id. at 18692–93. Under the 

Presumption Approach, a municipality’s selected CSO 

control program is presumed to meet the water quality-based 

requirements of the CWA if certain criteria are met. Those 

criteria include: no more than an average of four CSOs per 

year; the elimination or treatment of at least 85% of the 

volume of combined sewage collected during wet-weather 

events on an annual basis; and equivalent-to-primary 

treatment of CSOs (including removal of solids and 

floatables). Id. Under the Demonstration Approach, a 

municipality must demonstrate that its selected CSO 

controls will be adequate to meet WQS and protected 
12 CITY & COUNTY OF SAN FRANCISCO V. USEPA

designated uses of the receiving waters so as to satisfy the 

requirements of the CWA. Id. at 18693. When “natural 

background conditions or pollution sources other than 

CSOs” prevent WQS from being met, the LTCP must 

specify “a total maximum daily load” for the receiving 

waters. Id.

The CSO Control Policy creates a two-phase permitting 

process for municipalities with combined sewer systems. 

Phase I NPDES permits require the municipality to develop 

and implement the Nine Minimum Controls and to develop 

a LTCP. Id. at 18696. Phase II permits apply to the 

implementation of approved CSO controls, LTCPs, and 

post-construction monitoring. Id. Phase II permits must 

include provisions requiring the municipality to engage in 

ongoing modification and reassessment of their CSO control 

measures. Specifically, Phase II permits must include (1) 

“[a] requirement to reassess overflows to sensitive areas . . . 

based on consideration of new or improved techniques to 

eliminate or relocate overflows or changed circumstances 

that influence economic achievability” and (2) “[a] reopener 

clause authorizing the NPDES authority to reopen and 

modify the permit upon determination that the CSO controls 

fail to meet WQS or protect designated uses.” Id.

EPA subsequently issued a manual to aid NPDES 

permitting authorities in implementing the CSO Control 

Policy. U.S. Envt’l Prot. Agency, No. 832-B-95-008, 

Combined Sewer Overflows: Guidance for Permit Writers

(1995) (“CSO Guidance”). The CSO Guidance notes that 

“[a]lthough the two-phased [NPDES permitting] approach 

may be appropriate if a permittee has not implemented any 

CSO controls, in many instances, the separation between 

permit phases may not be distinct and permits may contain 

both Phase I and Phase II elements.” Id. at 2-2. For example, 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 13

under the CSO Control Policy, a Phase II permittee may be 

required to submit a revised LTCP containing “additional 

controls” if the NPDES authority determines WQS are not 

being met or designated uses are not being protected. 59 

Fed. Reg. at 18696. After a municipality has finished 

construction of all the CSO control measures required in a 

Phase II permit, it may be issued a “post-Phase II permit,” 

which includes post-construction compliance monitoring 

program requirements to provide ongoing assessment to 

determine whether the selected controls “are achieving 

compliance with applicable State water quality standards.” 

CSO Guidance, supra, at 5-2.

The CSO Control Policy includes exemptions for 

communities that, like San Francisco, developed and began 

implementing a CSO control plan prior to adoption of the 

Policy in 1994. 59 Fed. Reg. at 18690. Under Section I.C.1 

of the Policy, communities that had “completed or 

substantially completed construction” of their CSO controls 

are exempt from “the initial planning and construction 

provisions” of the Policy, but not from the “operational plan 

and post-construction monitoring provisions.” Id. The 

Section I.C.1 exemption further provides: “If, after 

monitoring, it is determined that WQS are not being attained, 

the permittee should be required to submit a revised CSO 

control plan that, once implemented, will attain WQS.” Id. 

Under Section I.C.2, municipalities that had “substantially 

developed” their CSO control program at the time the Policy 

issued are to “complete those facilities without further 

planning activities,” but they are not exempt from the postconstruction monitoring provisions of the policy. Id. 

Section I.C.3 of the Policy specifies that “[i]n the case of any 

ongoing or substantially completed CSO control effort, the 

NPDES permit . . . should be revised to include all 
14 CITY & COUNTY OF SAN FRANCISCO V. USEPA

appropriate permit requirements consistent with Section 

IV.B. of this Policy.” Id. Section IV.B.2.e of the Policy sets 

forth the requirement that Phase II permits include 

provisions for the ongoing reassessment of overflows to

sensitive areas. Id. at 18696. 

B. San Francisco’s Oceanside Wastewater System

San Francisco has two combined sewer systems and 

treatment facilities—“Bayside” and “Oceanside.” The 

Bayside wastewater system discharges into the San 

Francisco Bay from the Eastern side of the city and is 

authorized under an NPDES permit issued solely by the 

California Regional Water Quality Control Board for the San 

Francisco Bay Region (“Regional Water Board”). That 

permit is not before us. The permit before us is San 

Francisco’s NPDES permit for its Oceanside wastewater 

system, which discharges from the Western side of the city 

into the Pacific Ocean at points under state and federal 

jurisdiction and is thus authorized jointly by the Regional 

Water Board and the U.S. EPA. 

San Francisco’s Oceanside system includes the 

Oceanside Water Pollution Control Plant, 250 miles of 

combined sewers, and the Westside Recycled Water Project. 

Oceanside serves approximately 250,000 residents. San 

Francisco is authorized to discharge from Oceanside into the 

Pacific Ocean at eight discharge points. The primary 

discharge point, Discharge Point No. 001, the “Southwest 

Ocean Outfall,” is more than three miles from the shore, in 

United States waters. The remaining seven discharge points, 

CSD-001 through CSD-007, known as “combined sewer 

discharges” or “CSDs,” are located close to the shore, in 

State waters. CSD-001 through CSD-007 are used when 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 15

CSOs exceed the capacity of Discharge Point No. 001 during 

wet weather. 

Under normal conditions, water in the Oceanside system 

receives both primary and secondary treatment prior to 

discharge. During heavy rains, however, combined waste 

and storm water can exceed the system’s total 65 million 

gallons per day capacity and can be discharged prior to 

receiving primary or secondary treatment at the Oceanside 

plant. In such cases, wastewater receives only “equivalentto-primary treatment,” which includes “skimming of 

floatable solids,” prior to discharge. Four of the seven 

Oceanside CSD outfalls are connected to transport and 

storage structures that facilitate solid waste removal; 

however, three outfalls are not so connected. 

1. History of San Francisco’s CSO Control

San Francisco started work on its CSO control plan in 

the late 1960s, before the passage of the CWA in 1972. In 

1967, San Francisco was one of the first municipalities in the 

nation to “characterize” its CSOs and to recommend 

improvements in treatment. San Francisco developed a 

Master Plan for its wastewater management in 1971, which 

included automated monitoring of rainfall and sewer levels, 

creating a computational model of the sewer system, and 

conducting studies to assess water quality. The Master Plan 

also proposed a set of controls to reduce the city’s annual 

CSO frequency from eighty-two to eight. 

After the CWA was enacted, San Francisco modified its 

Master Plan in order to become eligible for federal 

construction grants. The 1974 revised Master Plan was 

accompanied by an Environmental Impact Report and 

Environmental Impact Statement prepared by EPA and San 

Francisco that described the environmental impacts of the 
16 CITY & COUNTY OF SAN FRANCISCO V. USEPA

alternatives for wastewater disposal, including CSOs. In 

1976, the Regional Water Board issued a series of permits 

and orders requiring the city to construct facilities to achieve 

its selected wet-weather controls. 

The California State Water Board adopted the Water 

Quality Control Plan for Ocean Waters of California

(“Ocean Plan”) in 1972, and has amended it several times, 

most recently in 2019. The Ocean Plan establishes WQS and 

effluent limitations for the Pacific Ocean within California’s 

jurisdiction in order to protect the “beneficial uses” of the 

waters. These beneficial uses include industrial water 

supply, recreation, fishing, and marine habitat. The Ocean 

Plan’s standards, along with the Water Quality Control Plan 

for the San Francisco Bay Basin (“Basin Plan”), are the 

applicable state WQS for San Francisco’s discharges into the 

Pacific Ocean under the CWA. See 33 U.S.C. 

§§ 1311(b)(1)(C), 1370; 40 C.F.R. §§ 122.4(d), 

122.44(d)(1), 131.4(a).

In 1979, California State Water Board Order No. 79-16 

(“1979 Ocean Plan Exception”) gave San Francisco a limited 

exception to the Ocean Plan for its wet-weather CSOs. The 

State Water Board recognized that San Francisco’s 

“continued use of the wet weather diversion structures” 

would violate the Ocean Plan’s water quality objectives, 

general management requirements, effluent quality 

requirements, and discharge prohibitions. The 1979 Ocean 

Plan Exception exempts San Francisco from compliance 

with the Ocean Plan during wet weather, allowing an 

average of eight CSO discharges per year. It requires that 

San Francisco post warning signs on all recreational beaches 

affected by CSOs and in all areas where shellfish is 

harvested during periods when the bacteriological standards 

of the Ocean Plan are not met. The 1979 Ocean Plan 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 17

Exception left the door open for the Regional Water Board 

to modify the terms of the exception: “[I]f the Regional 

Board finds that changes in location, intensity or importance 

of affected beneficial uses . . . have occurred, it may require 

the construction of additional facilities or modification of the 

operation of existing facilities.” EPA approved the 

exception in 1979 and the exception was continued in the 

last state Ocean Plan in 2019. 

In reliance on the 1979 Ocean Plan Exception permitting 

its wet-weather sewage discharges into the Pacific Ocean, 

San Francisco built the Oceanside CSD transport and storage 

structures and other CSO controls in the early 1980s. San 

Francisco completed construction in accordance with its 

city-wide Master Plan, including the Oceanside facilities, in 

1997 at a cost of $1.4 billion. From 1997–2018, Oceanside 

averaged fewer than its authorized eight CSOs per year from 

each discharge point. 

2. Prior Oceanside NPDES Permits

In 1997, EPA and the Regional Water Board issued San 

Francisco its first NPDES permit for Oceanside. The 1997 

permit stated that because San Francisco’s construction 

projects to control CSOs were “substantially complete,” it 

was exempt from the “planning and construction 

requirements” of the Policy. The permitting authorities 

determined that San Francisco’s CSO control program 

adhered to the CSO Control Policy through the city’s: (1) 

implementation of the Nine Minimum Controls; (2) 

substantial completion of control program construction such 

that a new long-term control plan (“LTCP”) was not 

necessary under Section I.C of the CSO Control Policy; (3) 

compliance with the CSO Control Policy’s “Presumption’ 

Approach” for ensuring water quality during wet weather; 
18 CITY & COUNTY OF SAN FRANCISCO V. USEPA

(4) appropriate consideration of “sensitive areas”; and (5) 

operation of the Oceanside Water Pollution Control Plant at 

maximum capacity during wet weather. The 2003 

Oceanside NPDES permit reflected a similar finding that 

San Francisco’s LTCP complied with the “Presumption 

Approach” outlined in the CSO Control Policy, and it 

ordered continued implementation of the city’s LTCP. The 

2009 Oceanside NPDES permit, the last permit issued by the 

EPA and the Regional Water Board prior to the challenged 

permit, reflected the agencies’ determination that San 

Francisco’s CSO control program “long term plan” was 

“consistent” with the national CSO Control Policy’s LTCP 

requirements. The 2009 permit expired in 2014, but because 

San Francisco “timely submitted a permit application,” the 

2009 permit continued in effect until issuance of a new 

permit. 

In 2011, San Francisco launched a Sewer System 

Improvement Program, a 20-year, nearly $7 billion 

investment initiative to enhance the reliability and 

performance of its wastewater system. This program 

included major capital improvements to the Oceanside 

facilities, including “the construction of the Westside 

Recycle Water Project, upgrades to the sludge handling 

facilities at the Oceanside Water Pollution Control Plant, and 

upgrades to the Westside Pump Station.” As part of the 

improvement program, San Francisco also conducted 

studies, including cost-benefit analyses, evaluating the 

feasibility of further reducing CSO discharges to public 

beaches. 

As presently constituted, San Francisco’s LTCP is not a 

single document. Rather, it is a collection of twenty-three 

documents. In 2018, San Francisco prepared a summary of 

these documents in San Francisco Wastewater Long Term 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 19

Control Plan Synthesis (“LTCP Synthesis”). San Francisco 

submitted the LTCP Synthesis to the Regional Water Board 

as part of the NPDES permitting process for its Bayside 

facilities. Excluding two 1994 documents that were 

applications for grandfathering status as part of San 

Francisco’s 1994 NPDES application for Bayside, the LTCP 

includes twenty-one separate planning documents, with 

dates ranging between 1967 and 1991. San Francisco 

explained in its introduction to the LTCP Synthesis that its 

“process of planning for, designing, and constructing 

projects to minimize and control wet weather discharge was 

iterative and extended for nearly two decades.” Therefore, 

according to San Francisco, “no single report describes the 

analyses and assumptions underlying the construction of the 

City’s current facilities.” 

3. Challenged NPDES Permit

EPA and the Regional Water Board reissued San 

Francisco’s Oceanside NPDES permit on December 10, 

2019. The permit sets forth, inter alia, specific dry-weather 

technology and water quality-based effluent limitations 

(“WQBELs”) for Oceanside. The permit specifies that 

“[d]uring wet weather, the Discharger shall comply with the 

narrative water quality-based effluent limitations contained 

in Provision VI.C.5.c (Long-Term Control Plan).” 

San Francisco petitions for review of two sets of 

provisions included in its 2019 Oceanside NPDES permit: 

(1) two general narrative prohibitions against violating 

applicable WQS for receiving waters (Section V and 

Attachment G; Section I.I.1); and (2) a requirement that San 

Francisco update its LTCP (Section VI.C.5.D).
20 CITY & COUNTY OF SAN FRANCISCO V. USEPA

First, the narrative prohibition in Section V provides:

Discharge shall not cause or contribute to a 

violation of any applicable water quality 

standard (with the exception set forth in [the 

1979 Ocean Plan Exception]) for receiving 

waters adopted by the Regional Water Board, 

State Water Resources Control Board (State 

Water Board), or U.S. EPA as required by the 

CWA and regulations adopted thereunder. If 

more stringent water quality standards are 

promulgated or approved pursuant to CWA 

section 303, or amendments thereto, the 

Regional Water Board and U.S. EPA may

revise or modify this Order in accordance 

with the more stringent standards. 

The narrative prohibition in Attachment G titled, “Regional 

Standard Provisions, and Monitoring and Reporting 

Requirements,” provides: “Neither the treatment nor the 

discharge of pollutants shall create pollution, contamination, 

or nuisance as defined by California Water Code section 

13050.” 

Second, for the first time since the 1990s, San Francisco 

is required to update its LTCP. Table 7 of the permit lists 

five major tasks that San Francisco must undertake to 

comply with this requirement: (1) Post-Construction 

Characterization, Monitoring, and Modeling of Combined 

Sewer System; (2) Public Participation; (3) Consideration of 

Sensitive Areas; (4) Operational Plan; (5) Post-Construction 

Compliance Monitoring Program. 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 21

C. Agency Proceedings

1. Early Drafts of the Oceanside NPDES Permit

EPA and the Regional Water Board shared an early draft 

of the challenged NPDES permit with San Francisco in 2014 

and received comments from San Francisco in January 2015. 

Both of the challenged general narrative prohibitions were 

present in the initial draft, though in slightly different form 

than in the final permit. Notably, the draft Section V 

limitations on receiving waters included, in addition to the 

general narrative prohibition, more detailed limitations than 

in the final permit. San Francisco suggested revising the 

Section V narrative prohibition so that it was limited to “dryweather” discharges from Discharge Point No. 001; the city 

did not comment on the Attachment G narrative prohibition. 

The initial draft text regarding San Francisco’s “Long-Term 

Control Plan Re-Evaluation” also differed from the LTCP 

required in the final permit. Notably, the initial draft permit 

conditioned the requirement that the LTCP be updated on the 

issuance of a prior determination by the permitting agencies 

that San Francisco’s discharges had violated applicable 

WQS. 

In February 2016, EPA requested more information from 

San Francisco about its CSOs “[f]ollowing reports that raw 

sewage mixed with stormwater was overflowing . . . into 

streets, sidewalks, residences and businesses.” EPA alleged 

that San Francisco had failed to include notice of several 

“widely reported” December 2014 “excursions” in its annual 

report to the Regional Water Board. (EPA defined 

“excursion” as “the exit of raw sewage or raw sewage mixed

with stormwater from the collection system.”) In November 

2017, the Regional Water Board requested additional 
22 CITY & COUNTY OF SAN FRANCISCO V. USEPA

monitoring data in order to better understand the city’s 

compliance with wet- and dry-weather discharge limitations.

In September 2018, after San Francisco submitted its 

LTCP Synthesis as part of the Bayside NPDES permitting 

process, the Regional Water Board found that the document 

did not satisfy the minimum required elements of an LTCP 

under its permit or under the CSO Control Policy. 

Specifically, the Regional Water Board found that the LTCP 

Synthesis failed to: (1) “reflect current circumstances,” 

because it did not incorporate the findings of several of the 

city’s own sewer system and CSO field studies and planning 

documents from 2013, 2014, and 2015; (2) “set forth any 

new operational requirements” “to optimize system 

operations so as to maximize pollutant removal during wet 

weather and minimize combined sewer discharges”; (3) “set 

forth additional measures, to the extent technically and 

economically feasible, to maximize pollutant removal and 

minimize combined sewer discharges”; (4) “develop or 

propose any metrics to evaluate the performance of its wet 

weather disinfection systems” for its discharge points; and 

(5) “propose a plan for post-construction compliance 

monitoring of all wet weather discharges” consistent with 

the CSO Control Policy. 

San Francisco responded by acknowledging the 

Regional Water Board’s concerns about its LTCP. It 

recognized that the Regional Water Board was likely to 

include new LTCP requirements in the soon-to-be reissued 

Oceanside NPDES permit. San Francisco explained that, for 

that reason, it was “particularly interested” in reaching a 

mutual understanding with the Regional Water Board about 

the “LTCP-related permit terms” so as to “avoid[] future 

miscommunications.” 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 23

In October 2018, EPA and the Regional Water Board 

shared another draft permit with San Francisco. The 

narrative provisions were unchanged from the initial draft. 

San Francisco again requested that the Section V prohibition 

be limited to dry-weather discharges from Discharge Point 

No. 001, and did not comment on the general provision in 

Attachment G. However, the October 2018 draft included a 

revised “LTCP Update” provision, detailing the major tasks 

San Francisco would need to perform to update its LTCP. 

This revised draft also made the LTCP update 

nonconditional. In response, San Francisco commented that 

the entire LTCP Update provision “[r]equires further 

discussion.” The draft permit was revised further, and San 

Francisco continued to suggest major changes to the draft 

regarding the proposed narrative prohibition in Section V 

and the LTCP Update provision. Representatives of San 

Francisco met with representatives of both agencies nine 

times between October 2018 and September 2019. 

2. Public Notice and Comment

In April 2019, EPA and the Regional Water Board 

published a draft Oceanside NPDES permit and solicited 

public comments. The published draft permit included the 

general narrative provisions of Section V, Attachment G, 

and the LTCP update requirement, that are largely consistent 

with their final form. The only material difference in the 

final draft was that the timeline for San Francisco’s 

compliance with the LTCP update requirement was 

extended by up to two years. 

On April 15, 2019, EPA issued a memorandum detailing 

its legal and factual bases for requiring San Francisco to 

update its LTCP. EPA stated that a number of changes to 

San Francisco’s combined sewer system, including San 
24 CITY & COUNTY OF SAN FRANCISCO V. USEPA

Francisco’s own capital upgrades, as well as its maintenance 

and operational problems, necessitated an LTCP update. 

EPA included in its memorandum a table listing cities, 

including New York City, Washington, D.C., and 

Philadelphia, that had recently updated their respective 

LTCPs.

San Francisco submitted detailed comments about the 

narrative water quality provisions in Section V and 

Attachment G, as well as the requirement that the LTCP be 

updated. San Francisco wrote that “[t]he generic, boilerplate 

narrative water-quality based permit terms are contrary to 

law and are unsupported by the available facts.” It also 

wrote that it “strongly disagrees that an update to the City’s 

LTCP is needed or appropriate.” Members of the public 

submitted comments to EPA and Regional Water Board. 

Many of the comments expressed concern about CSO 

discharges into private homes and businesses.

EPA and the Regional Water Board responded to San 

Francisco’s comments, defending their inclusion of narrative 

water quality standards in Section V and Attachment G as 

lawful under the CWA and federal regulations. In addition 

to asserting that such narrative provisions were lawful under 

the CWA, the agencies noted that EPA had included permit 

terms similar to those of Section V in other NPDES permits 

for combined sewer systems in other municipalities and for 

discharges into marine waters elsewhere in the United 

States. The Regional Water Board stated that it had included 

a provision identical to that in Attachment G “in nearly all 

individual NPDES permits since at least 1993.” 

EPA and the Regional Water Board also defended the 

requirement of an LTCP update, citing legal support and 

factual findings. The agencies stated that San Francisco is 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 25

not exempt “from planning requirements in perpetuity” 

under the CSO Control Policy. The agencies also explained 

their view that the current CSO discharges to Ocean Beach 

(CSD-001, CSD-002, CSD-003), China Beach (CSD-005), 

and Baker Beach (CSD-006 and CSD-007) affected 

“sensitive areas” because they discharge to “primary contact 

recreation waters” and “waters with threatened or 

endangered species.” These discharges therefore threaten 

the “beneficial uses” of the Pacific Ocean.

The agencies included the following four factual 

findings in their response: (1) between 2011 and 2014, 100 

million gallons of combined sewage and storm water were 

discharged from the Oceanside CSDs; (2) between 2008 and 

2014, surveys indicated 20% of recreational beach users 

were in contact with receiving water after CSOs; (3) between 

July 2012 and June 2013, 56 of 468 samples collected at 10 

shoreline monitoring locations exceeded water-quality 

criteria for at least one bacteria indicator, and 39 of those 

elevated samples (70%) were associated with a CSO event; 

and (4) between 2004 and 2014, pollutant concentrations 

(e.g., copper and zinc) in the CSOs exceeded water quality 

objectives. “Given these facts,” the agencies responded, “it 

is appropriate to assess ways to reduce the volume, 

frequency, and magnitude of the combined sewer discharges 

to sensitive areas to better protect beneficial uses.” 

3. Administrative Review of Final Permit

The Regional Water Board approved the final Oceanside 

NPDES permit (No. R2-2019-0028) on September 12, 

2019. EPA approved the permit (No. CA0037681) several 

months later, on December 10, 2019. 

After EPA approved the final permit in December 2019, 

San Francisco filed a petition for review of the permit with 
26 CITY & COUNTY OF SAN FRANCISCO V. USEPA

EPA’s Environmental Appeals Board (“EAB”). The EAB 

heard oral argument on October 8, 2020. San Francisco’s 

petition challenged the narrative prohibitions and the LTCP 

update requirement, contending that they are inconsistent 

with the CWA, its implementing regulations, and the facts in 

the record. San Francisco also challenged a provision 

regarding reporting of isolated CSOs, but it is not seeking 

judicial review of that provision. 

While San Francisco’s petition for review was pending 

before the EAB, the EPA stayed the contested provisions of 

the Oceanside permit. The EAB denied San Francisco’s 

petition for review in its entirety on December 1, 2020. City 

and County of San Francisco, 18 E.A.D. 322 (EAB 2020). 

EPA issued its Notice of Final Permit Decision on December 

22, 2020. The Oceanside NPDES permit became fully 

effective and enforceable on February 1, 2021. 

San Francisco timely petitioned for review in this court. 

We have jurisdiction to review EPA’s actions issuing or 

denying an NPDES permit under 33 U.S.C. § 1369(b)(1)(F). 

II. Standard of Review

The Administrative Procedure Act (“APA”) governs 

EPA’s issuance of NPDES permits. See Nat. Res. Def. 

Council v. U.S. EPA, 279 F.3d 1180, 1186 (9th Cir. 2002). 

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) 

(quoting Indep. Acceptance Co. v. California, 204 F.3d 

1247, 1251 (9th Cir. 2000)). “We may not substitute our 

judgment for that of the agency.” Food & Water Watch v. 

U.S. EPA, 20 F.4th 506, 514 (9th Cir. 2021). 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 27

An agency’s reasonable interpretation of a statute it 

administers is entitled to deference, Chevron, U.S.A., Inc. v. 

Nat. Res. Def. Council, Inc., 467 U.S. 837, 843–44 (1984), 

as is an agency’s reasonable interpretation of its genuinely 

ambiguous regulations, Kisor v. Wilkie, 139 S. Ct. 2400, 

2415–16 (2019). Furthermore, courts “must defer to a great 

extent to the expertise of the EPA” when reviewing the 

agency’s scientific determinations in an area within the 

agency’s expertise. Nat. Res. Def. Council, Inc. v. U.S. EPA, 

863 F.2d 1420, 1430 (9th Cir. 1988) (citing Balt. Gas & 

Elec. Co. v. Nat. Res. Def. Council, Inc., 462 U.S. 87, 103 

(1983)). 

III. Discussion

A. Narrative Prohibitions

San Francisco argues that two general narrative 

prohibitions included in the Oceanside NPDES permit, 

Section V and Attachment G, are unlawful because (1) they 

“contravene EPA’s obligation under the CWA to specify 

pollutant limits or operational requirements that will achieve 

compliance with WQS”; (2) by including these provisions in 

the permit, EPA failed to “follow its own rules” for setting 

WQBELs; and (3) EPA justified the need for the provisions 

“with only conclusory assertions.” 

For the convenience of the reader, we again quote the 

general narrative prohibitions. The first, Section V, 

“Receiving Water Limitations,” provides: 

Discharge shall not cause or contribute to a 

violation of any applicable water quality 

standard (with the exception set forth in [the 

1979 Ocean Plan Exception]) for receiving 

waters adopted by the Regional Water Board, 
28 CITY & COUNTY OF SAN FRANCISCO V. USEPA

State Water Resources Control Board (State 

Water Board), or U.S. EPA as required by the 

CWA and regulations adopted thereunder. If 

more stringent water quality standards are 

promulgated or approved pursuant to CWA 

section 303, or amendments thereto, the 

Regional Water Board and U.S. EPA may 

revise or modify this Order in accordance 

with the more stringent standards. 

The second, part of Attachment G, provides: “Neither the 

treatment nor the discharge of pollutants shall create 

pollution, contamination, or nuisance as defined by 

California Water Code section 13050.”1 

We address in turn San Francisco’s challenges to the 

general narrative prohibitions.

1. Consistency with the CWA

San Francisco argues that EPA’s inclusion of the general 

narrative prohibitions is inconsistent with the CWA because 

they are too vague to ensure the city’s control measures will 

protect water quality. We disagree.

1 Section 13050 defines “pollution” as “an alteration of the quality of the 

waters of the state by waste to a degree which unreasonably affects 

either . . . waters for beneficial uses [or] [f]acilities which serve 

beneficial uses.” Cal. Water Code § 13050(l). “Contamination” is “an 

impairment of the quality of the waters of the state by waste to a degree 

which creates a hazard to the public health through poisoning or through 

the spread of disease.” Id. § 13050(k). And “nuisance” is defined as 

“anything which . . . (1) [i]s injurious to health, or is indecent or 

offensive to the senses, or an obstruction to the free use of property . . . 

(2) [a]ffects at the same time an entire community or neighborhood, or 

any considerable number of persons . . . and (3) [o]ccurs during, or as a 

result of, the treatment or disposal of wastes.” Id. § 13050(m).
CITY & COUNTY OF SAN FRANCISCO V. USEPA 29

The plain text of the CWA and its implementing 

regulations provide NPDES permitting agencies with broad 

authority to impose limitations necessary to ensure the 

discharger’s adherence to “any applicable water quality 

standard.” 33 U.S.C. § 1311(b)(1)(C). Consistent with this 

statutory directive, federal regulations require all NPDES 

permits to include “any requirements in addition to or more 

stringent than promulgated effluent limitations guidelines or 

standards . . . necessary to . . . [a]chieve water quality 

standards established under section 303 of the CWA, 

including State narrative criteria for water quality.” 40 

C.F.R. § 122.44(d). The CWA and its implementing 

regulations thus require EPA to impose “any more stringent 

limitation” necessary to satisfy “State narrative criteria for 

water quality,” including those beyond “effluent 

limitations.” Id.; 33 U.S.C. § 1311(b)(1)(C). Moreover, the 

CSO Control Policy, which is legally binding under 33 

U.S.C. § 1342(q)(1), specifies that Phase I NPDES permits 

must include a provision requiring municipalities to 

“[c]omply with applicable WQS, no later than the date 

allowed under the State’s WQS, expressed in the form of a 

narrative limitation.” 59 Fed. Reg. at 18696 (emphasis 

added). These provisions do not merely authorize a 

permitting agency’s inclusion of narrative limitations on 

discharges that may violate state WQS; they require such 

narrative limitations when necessary to satisfy applicable 

WQS. 

Supreme Court precedent, our prior cases, and prior EAB 

decisions support the legality and confirm the enforceability 

of general narrative prohibitions in permits issued under the 

CWA. In PUD No. 1 of Jefferson County v. Washington 

Department of Ecology, 511 U.S. 700, 715–16 (1994), the 

Supreme Court upheld the state agency’s use of “open-
30 CITY & COUNTY OF SAN FRANCISCO V. USEPA

ended” criteria using “broad, narrative terms,” in addition to 

“numerical criteria,” to certify a hydroelectric power plant’s 

compliance with the CWA. In Northwest Environmental 

Advocates v. City of Portland, 56 F.3d 979, 989 (9th Cir. 

1995), a CSO case, we relied on Jefferson County to uphold 

citizen-suit enforcement of “water quality standards that are 

not translated into quantitative limitations.” We recognized 

that citizen suits to enforce such “qualitative regulations” are 

“an important enforcement tool,” especially in cases where 

effluent limitations either do not apply at all, or merely 

establish “minimum requirements.” Id. More recently, in 

Natural Resources Defense Council, Inc. v. County of Los 

Angeles, 725 F.3d 1194, 1199, 1205–07 (9th Cir. 2013), we 

enforced a narrative NPDES provision that was nearly 

identical to that of Section V, “Receiving Water 

Limitations,” in this case. Finally, in a closely analogous 

recent EAB decision, In re City of Lowell, 18 E.A.D. 115, 

176 (EAB 2020), the EAB held that EPA did not err in 

issuing a general, narrative NPDES permit provision 

“alongside more specific ‘end of pipe’ pollutant-specific 

effluent limits.” 

In the Oceanside NPDES permit at issue before us, EPA 

included, along with numeric effluent limitations for dryand wet-weather discharges, the two general narrative 

prohibitions quoted above, forbidding discharges that “cause 

or contribute to a violation of any applicable water quality 

standard,” or “create pollution, contamination, or nuisance.” 

The two narrative provisions are consistent with the CWA 

and its implementing regulations. They simply require that 

San Francisco’s discharges comply with applicable state 

WQS. Indeed, EPA points out that the language of Section 

V’s prohibition is frequently employed by EPA in other 

NPDES permits it issues for combined sewer systems, and 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 31

that the Attachment G provision is included in nearly all 

individual NPDES permits the Regional Water Board has 

issued over the past three decades. See Ohio Valley Env’t 

Coal. v. Fola Coal Co., 845 F.3d 133, 141–42 (4th Cir. 2017) 

(noting the frequency with which EPA imposes general 

narrative water quality standards in its NPDES permits and 

their consistent enforcement). 

San Francisco nevertheless contends that the general 

narrative provisions violate the CWA, arguing that the 

permit fails to provide the city with sufficiently clear 

directions as to how to ensure that its discharges comply with 

WQS. In support of its contention, San Francisco cites 

Natural Resource Defense Council v. U.S. EPA (“NRDC”), 

808 F.3d 556 (2d Cir. 2015). In that case, a narrative 

WQBEL—that is, a general narrative standard—mandated 

that ships “control discharges as necessary to meet 

applicable water quality standards in the receiving water 

body or another water body impacted by [the] discharges.” 

Id. at 568 (alteration in original) (quotation marks and 

citations omitted). The Natural Resources Defense Council 

(“NRDC”) challenged the narrative WQBEL on the ground 

that it was insufficient to satisfy EPA’s regulatory 

obligations under the CWA to ensure clean water. The 

Second Circuit agreed with NRDC, holding that the 

narrative provision, standing alone, was insufficient to 

satisfy EPA’s obligations under the CWA. The court wrote, 

“By requiring shipowners to control discharges ‘as 

necessary to meet applicable water quality standards’ 

without giving specific guidance on the discharge limits, 

EPA fails to fulfill its duty to ‘regulat[e] in fact, not only in 

principle.’” Id. at 578 (alteration in original) (citation 

omitted).
32 CITY & COUNTY OF SAN FRANCISCO V. USEPA

The case before us is the converse of NRDC. In that case, 

petitioner NRDC sought more stringent enforcement than 

the EPA permit required. Here, by contrast, San Francisco 

seeks less stringent enforcement. It seeks to turn NRDC on 

its head, relying on a decision requiring more effective 

enforcement to support an argument in favor of less effective 

enforcement. 

Even if we were to regard NRDC as a relevant precedent, 

we would conclude that the general narrative provision is 

consistent with the CWA. In contrast to the permit in NRDC, 

which contained only the two general narrative WQBEL 

provisions, see id. at 568, the Oceanside NPDES permit in 

the case before us includes several numeric and specific 

narrative WQBELs in addition to the challenged general 

narrative provisions. For example, the wet-weather 

discharge provisions in the Oceanside NPDES permit 

include specifications for the percentage of combined 

wastewater and storm water that Oceanside must capture 

during precipitation events; the specific flow rates that must 

be obtained prior to discharge from the different CSDs; and 

the percent chance of rain that triggers maximization of 

secondary treatment capacities. In other words, specific 

provisions in the Oceanside NPDES permit provide San 

Francisco with substantial guidance as to how to satisfy the 

applicable WQS. The challenged general narrative 

provisions operate as a “backstop” to those provisions, 

seeking to ensure that permitted discharges protect the water 

quality of the Pacific Ocean if the specific technological and 

water-quality based effluent limitations fail to achieve 

compliance with the CWA. 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 33

2. Conformity with Procedural Requirements

San Francisco also argues that the general narrative 

prohibitions are unlawful because EPA failed “to follow its 

own rules for setting WQBELs.” Specifically, San 

Francisco argues that EPA failed to follow the procedures 

set forth in 40 C.F.R. § 122.44(d)(1)(i)–(vii) when it 

formulated its general narrative provisions. In deciding San 

Francisco’s appeal within the agency, the EAB of EPA 

disagreed with San Francisco’s argument. The EAB wrote:

Although 40 C.F.R. § 122.44(d) sets forth a 

process for deriving pollutant-specific 

effluent limits when the permitting authority 

determines that a particular pollutant has the 

reasonable potential to cause or contribute to 

an exceedence of water quality standards, the 

regulations do not require all permit 

conditions necessary to meet water quality 

standards to be expressed in terms of specific 

pollutant-by-pollutant limitations.

We agree with the EAB. 

Under § 122.44(d)(1), NPDES permit limitations “must 

control all pollutants . . . which the Director determines are 

or may be discharged at a level which will cause, have the 

reasonable potential to cause, or contribute to an excursion 

above any State water quality standard, including State 

narrative criteria for water quality.” 40 C.F.R. 

§ 122.44(d)(1)(i). San Francisco reads this regulation as 

requiring EPA to “conduct a reasonable potential analysis” 

prior to setting any limitations—including general narrative 

prohibitions. San Francisco is mistaken. 
34 CITY & COUNTY OF SAN FRANCISCO V. USEPA

Section 122.44(d)(1) does not set forth an exclusive 

process for imposing WQBELs. The regulations in this 

section set forth minimum requirements for imposing 

pollutant-specific WQBELs. It does not state that the 

permitting authority cannot set general narrative limitations 

limits to achieve compliance with WQS. The governing 

statutory section, 33 U.S.C. § 1311(b)(1)(C), requires EPA 

to impose limitations “necessary” to meet “water quality 

standards” without restricting the agency to the sort of 

pollutant-by-pollutant regulation contemplated in 

§ 122.44(d)(1). We therefore conclude that EPA did not 

abuse its discretion or act contrary to §1311(b)(1)(C) in 

issuing its general narrative prohibitions.

3. Factual Basis for Narrative Provisions

San Francisco further contends that EPA arbitrarily 

imposed the contested narrative prohibitions based on “a pair 

of unsupported assertions,” namely (1) that the limits are 

“necessary to ensure compliance with applicable water 

quality standards,” and, relatedly, (2) that the prohibitions 

“serve as backstops in the event that the effluent 

limitations . . . prove to be inadequate.” San Francisco 

argues that the record demonstrates that the permit’s other 

effluent limitations “are sufficient to protect receiving water 

quality,” and that EPA’s decision to set WQBELs 

“necessarily included determinations that these Permit limits 

are sufficient to protect WQS on their own.” 

In response, EPA argues that the record supports its 

determination “that compliance with end-of-pipe numeric 

effluent limitations in the permit might not ensure 

compliance with water quality standards, including 

protection of beneficial uses.” EPA contends that because 

the CWA, under the binding CSO Control Policy, requires 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 35

that permit writers ensure municipalities’ “compliance with 

water quality standards and protection of designated uses,” 

the numeric effluent limitations for discharges may not be 

sufficient to ensure that wet-weather CSOs comply with the 

mandate to protect beneficial uses such as recreation. See 59 

Fed. Reg. at 18668 (emphasis added). In support, EPA cites 

evidence in the record of impairments to beneficial uses 

resulting from Oceanside’s wet-weather CSO discharges 

onto “popular recreational areas” including Ocean Beach, 

China Beach, and Baker Beach. 

Under the APA, an agency’s decision is arbitrary and 

capricious if it “offered an explanation for its decision that 

runs counter to the evidence before the agency.” Motor 

Vehicle Mfrs. Ass’n of U.S., Inc. v. State Farm Mut. Auto. 

Ins. Co., 463 U.S. 29, 43 (1983). An agency must “examine 

the relevant data and articulate a satisfactory explanation for 

its action including a ‘rational connection between the facts 

found and the choice made.’” Id. at 43 (quoting Burlington 

Truck Lines v. United States, 371 U.S. 156, 168 (1962)).

Here, in its response to San Francisco’s comments on the 

draft permit, EPA explained its decision to include the 

narrative provisions in Section V and Attachment G due to 

its concerns about San Francisco’s wet-weather CSOs. 

Specifically, the agency noted its determination that 

“particular assumptions about the frequency of combined 

sewer discharges” made by the State Water Board in its 1979 

Ocean Plan Exception order, which authorized Oceanside an 

average of eight CSOs per year, “may not ensure protection 

of beneficial uses today.” In response to another comment 

made by San Francisco (regarding the LTCP Update 

provision), EPA further cited factual evidence in support of 

its concern that current limitations in the Oceanside NPDES 

permit may not ensure the protection of “beneficial uses”—
36 CITY & COUNTY OF SAN FRANCISCO V. USEPA

namely that the combined sewer discharges at Ocean Beach, 

China Beach, and Baker Beach, while under the eight CSO 

per year limit, nevertheless may not adequately protect 

recreational use. 

Because EPA’s general narrative provisions were 

included as a “backstop” to ensure compliance with WQS 

not addressed by specific effluent limitations elsewhere in 

the permit—namely, protection of beneficial uses such as 

recreation—its decision is rationally supported by the 

evidence in the record describing negative impacts of CSOs 

on users of San Francisco’s beaches. 

4. Summary

We hold that EPA appropriately implemented the CWA 

by including the two challenged general narrative 

prohibitions in addition to more specific effluent limitations 

in the Oceanside NPDES permit; that EPA was not required 

to follow the procedures set forth in 40 C.F.R. § 122.44(d)(1) 

for deriving pollutant-specific effluent limitations in 

imposing the general narrative provisions; and that EPA’s 

decision to impose the general narrative provisions was 

rationally connected to evidence in the record indicating that 

a “backstop” to the more specific provisions would be useful 

in protecting beneficial uses. 

B. LTCP Update

San Francisco also challenges the Oceanside NPDES 

permit requirement that it update its LTCP for CSO control. 

For the convenience of the reader, we reiterate that the LTCP 

Update provision requires San Francisco to undertake five 

major tasks, including: (1) “characteriz[ing]” the updated 

combined sewer system; (2) describing its efforts to engage 

the public in its decision-making processes; (3) reporting on 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 37

its consideration of options to “eliminate, relocate, or reduce 

the magnitude or frequency of discharges to sensitive areas,” 

including cost/benefit analyses; (4) proposing an operational 

plan to minimize CSOs; and (5) submitting a revised postconstruction compliance monitoring program plan. 

San Francisco argues that: (1) EPA did not make a 

factual finding necessary to require San Francisco to update 

its LTCP under the CSO Control Policy; and (2) the 

requirement that San Francisco specifically address 

“sensitive areas” in the update exceeds the agency’s 

authority. 

We address San Francisco’s arguments in turn.

1. Factual Finding Supporting the LTCP Update 

Requirement

San Francisco argues that there is “only one 

circumstance when EPA can order an LTCP update: when 

the plan is not attaining compliance with WQS.” San 

Francisco argues that because EPA did not make a finding 

of noncompliance, the LTCP Update requirement is 

unlawful. 

It is undisputed that San Francisco was exempted from 

creating an initial LTCP in 1997. At that time San Francisco 

had “substantially completed” the construction of its CSO

control program facilities. The parties dispute whether San 

Francisco was exempted under Section I.C.1 or Section 

I.C.2. We agree with San Francisco that the Section I.C.1 

exemption was applied in its first NPDES permit. 
38 CITY & COUNTY OF SAN FRANCISCO V. USEPA

The Section I.C.1 exemption in the CSO Control Policy 

provides:

Any permittee that, on the date of publication 

of this final Policy, has completed or 

substantially completed construction of CSO 

control facilities that are designed to meet 

WQS and protect designated uses, and where 

it has been determined that WQS are being or 

will be attained, is not covered by the initial 

planning and construction provisions in this 

Policy; however, the operational plan and 

post-construction monitoring provisions 

continue to apply. If, after monitoring, it is 

determined that WQS are not being attained, 

the permittee should be required to submit a 

revised CSO control plan that, once 

implemented, will attain WQS. 

59 Fed. Reg. at 18690 (emphasis added). 

San Francisco argues that the final sentence of the 

Section I.C.1 exemption, italicized above, is the only basis 

on which a permitting agency may require an LTCP update 

from a city that was exempt from initial LTCP planning 

requirements. San Francisco cites in support of its argument 

the interpretative canon of expressio unius est exclusio 

alterius. It also relies on another provision of the CSO 

Control Policy, Section IV.B.2.g, the “reopener clause” 

provision, id. at 18696, arguing that “[t]he Policy expects no 

further planning or revisions to an approved LTCP, except 

‘upon determination that the CSO controls fail to meet water 

quality standards . . . .’” San Francisco also points to 

another EPA CSO Guidance manual from 1995, which 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 39

specifies that “[i]f post-construction monitoring indicates 

that existing WQS are not being met, the data generated can 

be used to identify the additional CSO controls necessary to 

achieve WQS.” U.S. Envt’l Prot. Agency, No. 832-B-95-

002, Combined Sewer Overflows: Guidance for Long-Term 

Control Plan 4-16 (1995).

EPA argues that a prior determination that WQS are not 

being met is not the only basis on which it may require an 

LTCP update. EPA cites provisions in the CSO Control 

Policy that grant EPA authority to reassess, modify, and 

require revisions to NPDES permits, even for those 

programs exempted from initial planning requirements, in 

support of its interpretation. 

Reading the CSO Control Policy as a whole, especially 

Section I.C, we agree with EPA. Most important, Section 

I.C.3 of the CSO Control Policy states: “In the case of any 

ongoing or substantially completed CSO control effort, the 

NPDES permit or other enforceable mechanism, as 

appropriate, should be revised to include all appropriate 

permit requirements consistent with section IV.B of this 

Policy.” 59 Fed. Reg. at 18690 (emphases added). We note 

that the Control Policy refers to Section IV.B without 

limitation, not just Section IV.B.2.g cited by San Francisco. 

Section IV.B sets forth all the NPDES permit requirements 

for CSOs. Id. at 18695–96. We read Section I.C.3 to provide 

NPDES permitting authorities with broad discretion to 

impose revised permit requirements, as set forth in Section 

IV.B, on municipalities initially exempted from planning 

and construction requirements under either Section I.C.1 

(exempting municipalities with “completed or substantially 

completed construction of CSO control facilities”) or 

Section I.C.2 (exempting municipalities with a 
40 CITY & COUNTY OF SAN FRANCISCO V. USEPA

“substantially developed” or ongoing “implement[ation]” of 

a CSO control program). Id. at 18690. 

Standard Phase II permit provisions set forth in the CSO 

Control Policy under Section IV.B further support EPA’s 

interpretation of Section I.C. The Policy mandates in 

Section IV.B.2.e that every Phase II permit—a permit given 

only to municipalities that have completed their LTCP and 

construction of their controls—include “[a] requirement to 

reassess overflows to sensitive areas in those cases where 

elimination or relocation of the overflows is not physically 

possible and economically achievable.” Id. at 18696. All 

Phase II permittees are to conduct a reassessment of their 

CSOs to sensitive areas “based on consideration of new or 

improved techniques to eliminate or relocate overflows or 

changed circumstances that influence economic 

achievability.” Id. In addition, as San Francisco 

acknowledges, the Policy mandates in Section IV.B.2.g that 

every Phase II NPDES permit include a “reopener clause 

authorizing the NPDES authority to reopen and modify the 

permit upon determination that the CSO controls fail to meet 

WQS or protect designated uses.” Id. (emphasis added). 

When an NPDES authority decides to modify a permit 

because “the CSO controls fail[ed] to . . . protect designated 

uses,” it can do so without necessarily having found a failure 

to attain WQS. These standard Phase II provisions 

demonstrate that even post-construction, the CSO Control 

Policy authorizes permitting agencies to order municipalities 

to periodically reassess their CSO control program for 

potential improvement with respect to designated uses, 

irrespective of any failure to meet WQS. 

Our dissenting colleague believes that Section

IV.B.2.g’s reference to “protecting ‘designated uses’ . . . 

adds nothing to the concept of achieving water quality 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 41

standards.” Dissenting Op. at 64. But the CSO Control 

Policy does not reference the “protect[ion] of designated 

uses” only in Section IV.B.2.g. The “protect[ion] of 

designated uses” language appears close to thirty times in the 

CSO Control Policy. Each time, the CSO Control Policy 

describes “protection of designated uses” as distinct from 

achieving water quality standards. For example, the Policy 

instructs permittees to “develop long-term CSO control 

plans which evaluate alternatives for attaining compliance 

with the CWA, including compliance with water quality 

standards and protection of designated uses.” 59 Fed. Reg. 

at 18688 (emphasis added). The Policy further advises that 

“[s]chedules for implementation of the long-term CSO 

control plan may be phased based on the relative importance 

of adverse impacts upon water quality standards and 

designated uses . . . .” Id. (emphasis added). The CSO 

Control Policy thus treats the “protection of designated uses” 

as an independently significant obligation, and not simply a 

byproduct of attaining the relevant water quality standard. 

We therefore hold that EPA’s ability to require San 

Francisco to update its LTCP is not conditioned on a finding 

that WQS were not being met. However, EPA’s requirement 

that San Francisco update its LTCP must be rationally 

supported by record evidence. See Motor Vehicle Mfrs. 

Ass’n of U.S., Inc. v. State Farm Mut. Auto. Ins. Co., 463 

U.S. 29, 43 (1983). We hold that there is adequate 

evidentiary support in the record. As we noted above, San 

Francisco’s current LTCP (a collection of twenty-one 

relevant documents) has not been updated since 1991, more 

than thirty years ago, despite San Francisco’s extensive 

investment in operational assessments and capital 

improvements through its Sewer System Improvement Plan 

since then. The fact that the LTCP is so outdated is enough, 
42 CITY & COUNTY OF SAN FRANCISCO V. USEPA

by itself, to support EPA’s conclusion that an updated LTCP 

is needed. Moreover, San Francisco’s current LTCP was 

found by the Regional Water Board to be inadequate to 

ensure compliance with the CWA. Evidence of these 

deficiencies in San Francisco’s current LTCP supports 

EPA’s requirement that San Francisco accurately 

characterize its contemporary sewer systems and evaluate 

control alternatives. In requiring an updated LTCP, EPA is 

ensuring that San Francisco satisfies applicable state WQS, 

most notably the 1979 Ocean Plan Exception, which was 

conditioned on San Francisco’s efforts to protect water 

quality “to the greatest extent practical,” taking into 

consideration “changes in location, intensity or importance 

of affected beneficial uses or demonstrated unacceptable 

adverse impacts [of the CSOs].” 

2. Requirement to Consider Sensitive Areas

San Francisco also contends that LTCP Update Task 3, 

one of its five assigned LTCP Update tasks, is “uniquely 

inconsistent with San Francisco’s exemption under Section 

I.C.1 of the Policy and EPA’s authority more generally.”

LTCP Update Task 3, “Consideration of Sensitive Areas,” 

requires that San Francisco reevaluate alternatives for the six 

of its seven CSD outfalls that are located adjacent to popular 

recreational beaches. Whereas the Section I.C.2 exemption 

explicitly provides that programs falling under this 

exemption “should be reviewed and modified to be 

consistent with the sensitive area, financial capability, and 

post-construction monitoring provisions of this Policy,” the 

Section I.C.1 exemption does not contain this provision for 

routine sensitive area reassessment. 59 Fed. Reg. at 18690. 

San Francisco argues that because it was granted an 

exemption under Section I.C.1 rather than I.C.2, “EPA 

cannot require the city to undertake any sensitive areas 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 43

analysis.” EPA argues that the CSO Control Policy provides 

it with authority to require San Francisco to reassess its 

CSOs to sensitive areas on an ongoing basis even assuming 

it was granted an exception from initial LTCP planning and 

construction under Section I.C.1 rather than Section I.C.2. 

Here, too, we agree with EPA. As discussed above, 

Section I.C.3 provides NPDES permitting authorities with 

broad discretion to impose revised permit requirements on 

municipalities initially exempted from planning and 

construction requirements under either Section I.C.1 or 

Section I.C.2 of the Policy. Id. at 18690. This discretion 

includes the ability to impose a requirement that 

municipalities reassess CSOs to sensitive areas. See id. at 

18696 (Section IV.B.2.e). The Policy mandates that all 

Phase II permits include a provision requiring a permittee to 

“reassess overflows to sensitive areas in those cases where 

elimination or relocation of the overflows is not physically 

possible and economically achievable.” Id. This 

reassessment requirement aligns squarely with the CSO 

Control Policy’s objective that “a permittee’s long-term 

CSO control plan . . . give the highest priority to controlling 

overflows to sensitive areas.” Id. at 18692. 

San Francisco contends that even if it were bound to 

reassess discharges into sensitive areas, the Task 3 

requirement stretches beyond EPA’s authority to require it 

to assess alternatives intended to “eliminate or relocate” 

CSOs. Id. In the view of San Francisco, EPA cannot instead 

require it to assess the alternative of “reducing the magnitude 

and frequency” of CSOs. However, alternative controls that 

would aid in “reducing the magnitude and frequency” of 

CSOs are likely to be less costly than alternatives that would 

entail relocating or eliminating CSOs altogether. We decline 

to overturn EPA’s interpretation of the CSO Control Policy, 
44 CITY & COUNTY OF SAN FRANCISCO V. USEPA

which allows it to require a less expensive and potentially 

more effective measure. 

3. Summary

In sum, the CSO Control Policy provides EPA with 

authority to require San Francisco to update its LTCP and 

reevaluate alternatives for its CSO discharges to sensitive 

areas. EPA’s decision to require an updated LTCP is 

rationally supported by evidence in the record, and we hold 

that EPA did not act unlawfully in including the provision in 

the 2019 Oceanside NPDES permit. 

Conclusion

We hold that EPA had authority under the CWA to 

include in the Oceanside NPDES permit two narrative 

prohibitions against violating applicable WQS; that EPA had 

authority to require San Francisco to update its LTCP for 

CSOs; and that EPA’s decisions were rationally connected 

to evidence in the record. We therefore deny San 

Francisco’s petition for review. 

Petition DENIED.
CITY & COUNTY OF SAN FRANCISCO V. USEPA 45

COLLINS, Circuit Judge, dissenting:

The City and County of San Francisco (“San Francisco”) 

challenges three specific conditions that the Environmental 

Protection Agency (“EPA”) included in the permit that the 

EPA issued to San Francisco, under the “National Pollutant 

Discharge Elimination System” (“NPDES”), in connection 

with the operation of a combined wastewater and stormwater 

collection and treatment system. In my view, all three 

conditions are invalid, and I would therefore grant San 

Francisco’s petition for review, vacate the challenged 

provisions, and remand the matter to the agency. Because 

the majority instead upholds each condition, I respectfully 

dissent.

I

To place the issues raised by the parties in their proper 

context, it is helpful first to provide some appropriate 

background concerning the Clean Water Act, the special

rules governing combined sewer systems, and the permit at 

issue here.

A

The current federal water pollution control system dates 

back to the enactment of the Federal Water Pollution Control 

Act Amendments of 1972, Pub. L. No. 92-500, 86 Stat. 816 

(1972). That Act, which itself is often colloquially called the 

Clean Water Act, completely rewrote the then-existing 

Federal Water Pollution Control Act (“FWPCA”). See City 

of Milwaukee v. Illinois, 451 U.S. 304, 317 (1981). The 

revised FWPCA—which was officially given the alternative 

title of the “Clean Water Act” in 1977, see Pub. L. No. 95-

217, § 2, 91 Stat. 1566 (1977)—remains, as amended, the 

principal federal statute governing the regulation and control 
46 CITY & COUNTY OF SAN FRANCISCO V. USEPA

of water pollution, and it has been classified to chapter 26 of 

the unenacted title 33 of the United States Code. See 33 

U.S.C. § 1251 et seq.

Prior to its amendment in 1972, the FWPCA “employed 

ambient water quality standards specifying the acceptable 

levels of pollution in a State’s interstate navigable waters as 

the primary mechanism in its program for the control of 

water pollution.” EPA v. California ex rel. State Water Res. 

Control Bd. (EPA v. California), 426 U.S. 200, 202 (1976). 

These overall standards for particular bodies of water were 

intended “to serve both to guide performance by polluters 

and to trigger legal action to abate pollution.” Id. But the 

system “proved ineffective” in practice. Id. Because the 

focus was on the ultimate aggregate level of pollution in the 

body of water as a whole, rather than on “the preventable 

causes of water pollution” into that body of water, 

enforcement of the standards required “work[ing] backward

from an overpolluted body of water to determine which point 

sources are responsible and which must be abated.” Id. at 

202, 204 (emphasis added). That feature, combined with 

“the awkwardly shared federal and state responsibility for 

promulgating such standards” and the “cumbrous 

enforcement procedures,” made it “very difficult to develop 

and enforce standards to govern the conduct of individual 

polluters.” Id. at 202–03. 

As the Supreme Court has explained, the Clean Water 

Act (“CWA”) takes an entirely different approach that 

includes two major changes. First, rather than measuring an 

individual polluter’s performance “against limitations 

derived from water quality standards to which it and other 

polluters must collectively conform,” the CWA directly 

regulates discharges from specific point sources by setting 

“effluent limitations”—i.e., “restrictions . . . on quantities, 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 47

rates, and concentrations of chemical, physical, biological, 

and other constituents which are discharged from point 

sources.” Id. at 204–05 (emphasis added). Second, to 

implement this shift to a direct regulation of discharges, the 

CWA “establish[ed] the National Pollutant Discharge 

Elimination System (NPDES) as a means of achieving and 

enforcing the effluent limitations.” Id. at 205 (footnote 

omitted). “Under the NPDES, it is unlawful for any person 

to discharge a pollutant without obtaining a permit and 

complying with its terms,” which include the applicable 

effluent limitations for the relevant point sources. Id.; see 

also 33 U.S.C. § 1311(a).

Thus, under the revised regulatory scheme established by 

the CWA, the regulators issuing individual NPDES permits 

are ultimately required to translate the overall water quality 

standards for a given body of water—which are typically set 

by States—into “obligations (including a timetable for 

compliance) of the individual discharger,” as expressed in 

that discharger’s NPDES permit. EPA v. California, 426 

U.S. at 205. The effluent limitations contained in an NPDES 

permit include, in the first instance, “technology-based 

limitations on individual discharges” from point sources. 

PUD No. 1 of Jefferson County v. Washington Dep’t of 

Ecology, 511 U.S. 700, 704 (1994); see also Our Children’s 

Earth Foundation v. EPA, 527 F.3d 842, 848 (9th Cir. 2008) 

(explaining that such “technology-based” effluent 

limitations are “determined according to the best available 

or practicable technology” for reducing pollution at the 

source); Natural Res. Def. Council, Inc. v. EPA (NRDC I), 

822 F.2d 104, 110 (D.C. Cir. 1987) (stating that 

“technology-based effluent limitations, as their name 

suggests, derive from standards formulated with reference to 

pollution control technology”). 
48 CITY & COUNTY OF SAN FRANCISCO V. USEPA

However, if such technology-based effluent limitations 

“are insufficient to attain or maintain water quality 

standards, the CWA requires NPDES permits to include 

additional water quality-based effluent limits.” Natural Res. 

Def. Council, Inc. v. EPA (NRDC II), 808 F.3d 556, 564 (2d 

Cir. 2015) (emphasis added). Such water-quality-based 

effluent limitations are set “based on the amounts and kinds 

of pollutants in the water in which the point source 

discharges,” NRDC I, 822 F.2d at 110, and they are set 

“without regard to cost or technological availability,” 

NRDC II, 808 F.3d at 565. In addition to such numericallybased effluent limitations, an NPDES permit may also 

contain “narrative” conditions that specify, in descriptive 

terms, how particular activities are to be conducted, so as to 

achieve compliance with the relevant water quality 

standards. PUD No. 1, 511 U.S. at 716.

The various specific limitations contained in the NPDES 

permit are then subject to “direct administrative and judicial 

enforcement.” EPA v. California, 426 U.S. at 205. But, 

“[w]ith few exceptions,” if an NPDES permit holder 

complies with the conditions of its permit, that discharger 

will be “deemed to be in compliance” with the principal 

provisions of the CWA. Id.; see also 33 U.S.C. § 1342(k). 

And that remains true even if the discharges released in 

compliance with the discharger’s NPDES permit “would 

reach waters already in violation of existing water quality 

standards.” Arkansas v. Oklahoma, 503 U.S. 91, 107 (1992). 

B

Operators of a combined wastewater and stormwater 

collection and treatment system—such as the one operated 

by San Francisco here—are subject to specialized rules that 

govern both the NPDES permitting process for such systems 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 49

and other aspects of their operation. A key objective of these 

special rules is to address the fact that such a “combined 

sewer system” (“CSS”), which “conveys sanitary 

wastewaters . . . and storm water through a single-pipe 

system” to a water-treatment plant, may on occasion 

experience a “combined sewer overflow” (“CSO”), i.e., a 

discharge “at a point prior” to treatment at the watertreatment plant. See Combined Sewer Overflow (CSO) 

Control Policy, 59 Fed. Reg. 18687, 18689 (Apr. 19, 1994) 

(emphasis added). Such an overflow can occur when, for 

example, heavy rains result in the system being 

overwhelmed by an increased flow of water that exceeds the 

capacity of the treatment plant. To help combat the dangers 

such CSOs pose, the EPA promulgated a special “CSO 

Control Policy” in 1994. Id. at 18687–97. Pursuant to a 

2000 amendment to the CWA, this CSO Control Policy 

document effectively has the force of a statute. See 33 

U.S.C. § 1342(q)(1) (requiring that “[e]ach permit, order, or 

decree issued” under the CWA, after December 21, 2000, 

“for a discharge from a municipal combined storm and 

sanitary sewer shall conform to the Combined Sewer 

Overflow Control Policy” issued in 1994).

The CSO Control Policy relies on two primary 

mechanisms for achieving its overall objectives of 

controlling and mitigating CSO events. First, under § II.C 

of the Policy, each permittee operating a system that 

experiences CSOs must “develop[] and implement[]” a 

“long-term CSO control plan[] that will ultimately result in 

compliance with the requirements of the CWA.” 59 Fed. 

Reg. at 18691. A full-blown long-term control plan 

(“LTCP”) would include, inter alia, (1) preliminary work, 

including public consultation, to identify and evaluate 

appropriate alternatives for building the infrastructure to 
50 CITY & COUNTY OF SAN FRANCISCO V. USEPA

achieve the objectives of the CSO Control Policy in a costeffective manner; (2) an implementation schedule for the 

selected alternatives, including a “construction and 

financing schedule”; and (3) “a post-construction water 

quality monitoring program.” Id. at 18691–94.

Second, the Policy relies on the NPDES permitting 

process to support both the LTCP process and the overall 

objectives of the Policy. Thus, § IV.B.1 of the Policy 

provides that, in the “Phase I” stage in which a permittee is 

developing an LTCP, the NPDES permit must contain 

specific conditions to ensure that the permittee, inter alia, 

(1) accomplishes the necessary tasks for developing and 

submitting an LTCP; and (2) immediately implements 

certain minimum controls. Id. at 18696. Section IV.B.2 of 

the Policy states that, at “Phase II,” the permit must contain 

various enumerated conditions, including: (1) appropriate 

“requirements for implementation of the long-term CSO 

control plan”; (2) requirements for appropriate monitoring; 

(3) a “requirement to reassess overflows to sensitive areas” 

under certain circumstances; and (4) a “reopener clause 

authorizing the NPDES authority to reopen and modify the 

permit upon determination that the CSO controls fail to meet 

WQS [i.e., water quality standards] or protect designated 

uses.” Id. Section IV.B.2.g specifically provides that, in the 

event of “such determination,” the “permittee should be 

required to develop, submit, and implement, as soon as 

practicable, a revised CSO control plan which contains 

additional controls to meet WQS and designated uses.” Id. 

C

San Francisco currently “provides wastewater treatment 

[services] for western San Francisco and a small portion of 

[nearby] Daly City”—a service area with a population 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 51

totaling approximately 250,000 people. It does so by way of 

its Oceanside Water Pollution Control Plant (the “Oceanside 

Plant”) and a combined sewer system that collects 

wastewater and stormwater and transports it to that plant. (I 

will refer to the Oceanside Plant and the combined sewer 

system, collectively, as the “Oceanside System”). The 

Oceanside System’s combined sewer system consists of 

“approximately 250 miles of pipe, one major pump station 

. . . six minor pump stations . . . and three large 

transport/storage structures.” Since 1997, San Francisco has 

discharged treated wastewater from its Oceanside System 

into the Pacific Ocean pursuant to the terms and conditions 

of successive NPDES permits that have been jointly issued 

by the EPA and the California Regional Water Quality 

Control Board for the San Francisco Bay Region (the 

“Regional Board”). In the 25 years prior to receiving its 

1997 NPDES Permit, San Francisco spent approximately 

$1.4 billion dollars fully implementing an integrated plan for 

wastewater management (the “Master Plan”) that it had 

begun developing in 1971—the latter being a time when San 

Francisco’s then-existing sewage and wastewater treatment 

systems were experiencing an average of 82 CSOs per year. 

The Master Plan was designed to reduce the average 

frequency of overflow events by approximately 90%, to just 

eight per year. 

Congress passed the CWA one year after San Francisco 

developed its 1971 Master Plan. In addition to the NPDES 

permitting regime described above, the CWA also 

established a construction grant program in which the EPA 

would provide States and municipalities with federal 

funding to cover significant portions of the construction 

costs for projects that “demonstrate[d] a new or improved 

method of preventing, reducing, and eliminating the 
52 CITY & COUNTY OF SAN FRANCISCO V. USEPA

discharge into any waters of pollutants from sewers which 

carry storm water or both storm water and pollutants.” 33 

U.S.C. § 1255(a). To be eligible for those funds, an 

applicant had to submit a “Facility Plan” to the EPA and to 

the State showing that its proposed project “complied with 

the National Environmental Policy Act.” Seeking to take 

advantage of this new grant program, San Francisco spent 

the next two years revising its Master Plan. As part of that 

process, an “Environmental Impact Report . . . and 

Environmental Impact Statement” were “prepared by the 

EPA and the San Francisco Department of Planning” and 

issued in 1974. 

The following year, the Regional Board adopted “the 

first comprehensive Basin Plan for the San Francisco Bay 

Region” and began issuing “a series of permits and orders 

that included enforceable schedules for implementing [San 

Francisco]’s selected wet weather controls,” which included 

“milestones for planning, design, and construction.” In 

particular, in March 1976, the Regional Board ordered San 

Francisco to construct facilities to “reduce the frequency of 

discharge” from “an average of 114 overflow events per year 

to an average of one overflow event per year” and to submit 

a “study to better define the costs and water quality benefits 

of facilities designed to achieve various overflow 

frequencies.” San Francisco completed the required study 

and submitted the results to the Regional Board on 

December 15, 1978, accompanied by a request that the 

Regional Board increase its maximum number of allowable 

overflow events from one per year to eight per year. That 

change required an exemption from the applicable “Water 

Quality Control Plan for Ocean Waters of California,” and 

the Regional Board granted the requested exemption on 

March 23, 1979, and the EPA approved it a few months later. 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 53

This exemption order, together with the revised Master Plan 

San Francisco adopted in 1980, “became the basis for all 

subsequent planning, design, and construction of” the 

Oceanside System. 

With these provisions in place, San Francisco began 

constructing the Oceanside System in the early 1980s and 

had fully implemented the revised Master Plan by 1997, at a 

total cost of approximately $1.4 billion in 1997 dollars. That 

same year, the EPA and the Regional Board jointly issued an 

NPDES Permit authorizing San Francisco to discharge 

pollutants from the Oceanside System into the Pacific Ocean 

from the System’s eight designated discharge points, 

provided that those discharges complied with the terms and 

conditions set forth in the permit. In that permit, the 

Regional Board and the EPA expressly found that, by 

implementing the Master Plan it had originally began 

developing in the 1970s, San Francisco had “substantially 

completed the wasterwater projects needed to control 

combined sewer overflows and to reduce water quality 

impact from the [Oceanside System]” and was thus “exempt 

from the planning and construction requirements” of the 

CSO Control Policy under § I.C.1 of that Policy. The EPA 

and the Regional Board also concluded that San Francisco 

had “otherwise demonstrated compliance with section I.C.1 

of the CSO Control Policy” and therefore was “not required 

to complete a (new) CSO long-term plan.” The 

administrative record elsewhere specifically reflects what is 

implicit in the 1997 permit’s findings, which is that San 

Francisco’s LTCP “is not a single document, as is the case 

with most combined sewer systems,” but rather “is a 

collection of documents” that were “developed over the 

course of two decades, dating from 1971.”
54 CITY & COUNTY OF SAN FRANCISCO V. USEPA

The Regional Board and the EPA subsequently renewed 

San Francisco’s NPDES Permit for the Oceanside System in 

2003 and 2009. In both permits it reiterated that San 

Francisco’s program was consistent with the CSO Control 

Policy and that San Francisco was not required to prepare a 

revised LTCP.

The most recent 2019 renewal of the NDPES permit for 

the Oceanside System included three conditions that, after 

exhausting its administrative remedies, San Francisco timely 

challenges here.

II

Two of the conditions challenged by San Francisco 

consist of narrative limitations that are based solely on 

whether the receiving waters are meeting the applicable 

water quality standards. First, § V of the permit prohibits the 

City from making any discharge that (1) “contribute[s]” to a 

violation of “any applicable water quality standard . . . for 

receiving waters” (emphasis added). Second, Provision I.I.1 

of Attachment G to the permit similarly states that San 

Francisco may not make a discharge that “create[s] 

pollution, contamination, or nuisance as defined by 

California Water Code section 13050.” Because § 13050 

defines the terms “pollution,” “contamination,” and 

“nuisance” in a manner that focuses on the overall condition 

of the receiving waters, San Francisco’s compliance with 

this condition likewise turns on that overall condition.1 In 

1 California Water Code § 13050(k) defines “[c]ontamination” as “an 

impairment of the quality of the waters of the state by waste to a degree 

which creates a hazard to the public health through poisoning or through 

the spread of disease,” and the term “includes any equivalent effect 

resulting from the disposal of waste, whether or not waters of the state 

are affected.” Similarly, “[p]ollution” is defined as “an alteration of the 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 55

my view, the EPA’s imposition of these narrative limitations 

was “arbitrary and capricious, an abuse of discretion, or 

otherwise not in accordance with law.” 5 U.S.C. 

§ 706(2)(A). I would therefore set aside these two 

conditions. 

A

These narrative limitations are inconsistent with the text 

of the CWA. Section 301(a)(1) requires the EPA to set 

specified types of “effluent limitations,” as well as “any 

more stringent limitation, including those [that are] 

necessary to meet water quality standards” established under 

applicable state or federal law or that are “required to 

implement any applicable water quality standard established 

pursuant to [the CWA].” 33 U.S.C. § 1311(b)(1)(C) 

(emphasis added). On its face, the statute draws an explicit 

distinction between the “limitations” that the agency must 

devise and impose on a particular permittee’s discharges and 

the overall “water quality standards” that govern the 

applicable waters into which those discharges will be made. 

The narrative conditions challenged here effectively ignore 

this critical distinction by making the ultimate, overall 

quality of the waters of the state by waste to a degree which unreasonably 

affects either”: (1) “[t]he waters for beneficial uses,” or (2) “[f]acilities 

which serve th[o]se beneficial uses.” Id. § 13050(l)(1)(A)–(B). And 

“‘[n]uisance’ means anything which meets all of the following 

requirements”: (1) it “[i]s injurious to health, or is indecent or offensive 

to the senses, or an obstruction to the free use of property, so as to 

interfere with the comfortable enjoyment of life or property”; (2) it 

“[a]ffects at the same time an entire community or neighborhood, or any 

considerable number of persons, although the extent of the annoyance or 

damage inflicted upon individuals may be unequal”; and (3) it “[o]ccurs 

during, or as a result of, the treatment or disposal of wastes.” Id. 

§ 13050(m)(1)–(3).
56 CITY & COUNTY OF SAN FRANCISCO V. USEPA

“water quality standards” themselves the applicable 

“limitation” for an individual discharger.

Moreover, the agency’s erasure of this crucial distinction 

is fundamentally inconsistent with the CWA’s regulatory 

approach. As explained earlier, see supra section I(A), the 

CWA largely rejected the prior ex post system of “work[ing] 

backward from an overpolluted body of water” in favor of 

an ex ante system of fashioning, using the agency’s 

expertise, the “direct restrictions on discharges” that are 

needed to achieve the overall water quality standards for the 

relevant waters. EPA v. California, 426 U.S. at 204–05; see 

also City of Milwaukee v. Illinois, 451 U.S. at 320–21. 

Indeed, the agency generally must rely, in the first instance, 

on technology-based effluent limitations that regulate 

discharges at the point source. See Our Children’s Earth 

Foundation, 527 F.3d at 848. If those are inadequate, then 

the agency can work backward from the applicable water 

quality standards to fashion, for the relevant dischargers, 

“any more stringent limitations” on discharges that are 

necessary to meet those standards. 33 U.S.C. 

§ 1311(b)(1)(C); see also EPA v. California, 426 U.S. at 205 

n.12 (noting that, if technology-based effluent limitations are 

inadequate, “[w]ater quality standards are retained as a 

supplementary basis for effluent limitations”); NRDC II, 808 

F.3d at 577–78 (similar). Here, by failing to articulate any 

“specific guidance” as to the “practices” or “procedures” that 

dischargers should undertake, NRDC II, 808 F.3d at 578–79, 

and by instead directing the permittee to figure out how to 

ensure compliance with the water quality standards, the 

agency has effectively required the permittee to ensure that 

its discharges—taken together with any other sources of 

pollution into the applicable waters—do not result in a 

breach of the applicable water quality standards. In doing 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 57

so, the agency has fundamentally abdicated the regulatory 

task assigned to it under the CWA. See id. (holding that a 

similar narrative condition reflected a failure of the agency 

“to fulfill its duty to regulate in fact, not only in principle”). 

As the Second Circuit explained in invalidating a similar 

condition, this analysis is further confirmed by § 402 of the 

CWA, which governs the issuance of NPDES permits. See

NRDC II, 808 F.3d at 579–80. That section states that the 

conditions fashioned by the agency for a given permit must 

“assure compliance” with the relevant requirements of the 

CWA, including the achievement of the applicable water 

quality standards. See 33 U.S.C. § 1342(a)(2). The agency 

can “hardly” be said to have satisfied that obligation when it 

issues a generic instruction not to let the water quality 

standards be violated, because such a mere recitation of the 

ultimate objective “in fact adds nothing” in terms of 

specifying meaningful permit conditions that will “assure” 

ex ante compliance with the water quality standards. 

NRDC II, 808 F.3d at 578. Even if crafting such conditions 

is “difficult,” the EPA “cannot simply give up and refuse to 

issue more specific guidelines.” Id. at 578. Including the 

sort of generic narrative condition employed here therefore 

“violate[s]” § 402’s “requirement that NPDES permits 

ensure compliance with the CWA.” Id. at 580. 

I hasten to add that there is one limited sense in which 

this generalized narrative condition does provide specific 

guidance, but it is the proverbial exception that proves the 

rule. In the case of a body of water that, for whatever reason 

(e.g., pollution from another source), happens to contain 

pollution levels that exceed the applicable water quality 

standards, the inclusion of such a narrative condition would 

automatically make unlawful any further discharges of the 

same pollutant into those waters. That is, because any such 
58 CITY & COUNTY OF SAN FRANCISCO V. USEPA

further discharges into a body of water that is already out of 

compliance would necessarily “contribute” to a violation of 

“any applicable water quality standard . . . for receiving 

waters,” any such discharges would violate that generic 

permit condition and would therefore be unlawful under the 

CWA. That would automatically trigger the “crushing 

consequences” that the CWA provides “even for inadvertent 

violations.” Sackett v. EPA, 143 S. Ct. 1322, 1330 (2023). 

Even negligent discharges in violation of a permit condition 

can lead to “severe criminal penalties including 

imprisonment,” as well as substantial civil penalties that 

“can be nearly as crushing as their criminal counterparts.” 

Id. (citing 33 U.S.C. § 1319(c)). Routine inclusion of such 

a narrative condition in permits would thus automatically

require, in the event of excessive pollution from another 

source, the immediate cessation of discharges involving the 

same pollutant from all other sources, without regard to the 

importance of those sources’ operations or, indeed, any other 

consideration. But as the Supreme Court unanimously held 

in Arkansas v. Oklahoma, the CWA has never been 

construed as “mandat[ing] a complete ban on discharges into 

a waterway that is [already] in violation of [water quality] 

standards.” 503 U.S. at 108. As the Court noted, such an 

automatic ban on any other discharges might impede other 

important and competing objectives of the CWA. Id. 

Application of regulatory judgment, using the “broad 

authority” vested in the agency to address such a situation, 

is more consistent with achieving the overall objectives of 

the CWA than an automatic prohibition on any and all 

discharges involving waters that, for whatever reason, may 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 59

happen to be out of compliance with water quality standards. 

Id.

2

Accordingly, I would vacate these two narrative 

conditions, which are “arbitrary and capricious, an abuse of 

discretion, or otherwise not in accordance with law.” 

5 U.S.C. § 706(2)(A). 

B

The various reasons offered by the majority for its 

contrary conclusion all lack merit.

First, the majority notes that the Supreme Court in PUD 

No. 1 upheld the inclusion of NPDES permit limitations that 

use “broad, narrative terms.” See Opin. at 30 (quoting PUD 

No. 1, 511 U.S. at 716). But that general proposition does 

not address the further question of whether this particular 

narrative limitation is consistent with the CWA. The Court’s 

endorsement of broadly framed narrative conditions simply 

does not support the agency’s wholesale erasure of the 

distinction between the “limitations” to be crafted by the 

agency and the ultimate water quality standards those 

limitations are supposed to help to achieve. Indeed, the 

contrast between the narrative conditions in this case and 

2 The majority is therefore quite wrong when it goes further and says 

that, not only is such a narrative condition consistent with the CWA, it 

is “require[d]” by that statute. See Opin. at 29. That holding—viz., that 

the CWA mandates such a prohibition on further discharges into a body 

of water that is not compliant with applicable water quality standards—

is flatly contrary to Arkansas v. Oklahoma. The majority is likewise 

wrong in contending that the transitional provisions of the CSO Control 

Policy that govern “Phase I” permits required the inclusion of such a 

narrative condition in this case. See Opin. at 29. Even assuming 

arguendo that the majority’s construction of the relevant Phase I 

provision were correct, it is irrelevant to the Phase II permit at issue here.
60 CITY & COUNTY OF SAN FRANCISCO V. USEPA

those in PUD No. 1 only underscores this critical difference: 

the specific limitation that the Court upheld in PUD No. 1

was not a vague instruction to ensure that water quality 

standards were ultimately met, but a specific instruction to a 

proposed hydroelectric project to maintain, in the river from 

which the water was taken, “a minimum stream flow 

requirement of between 100 and 200 [cubic feet per second] 

depending on the season.” 511 U.S. at 709. 

Second, the majority contends that this court’s prior 

decisions have already upheld the validity of including such 

a narrative condition in an NPDES permit. See Opin. at 30. 

That is wrong. In the two cases cited by the majority, the 

only question that was presented and resolved was whether, 

in a situation in which such a condition has already been 

included in a permit that has not been challenged by the 

permittee, that condition is enforceable by private parties by 

way of an action under § 505 of the CWA. See Northwest 

Env’t Advocs. v. City of Portland, 56 F.3d 979, 990 (9th Cir. 

1995) (holding that CWA § 505(a) “confer[s] jurisdiction 

for citizen suits to enforce water quality standards when they 

are conditions of a CWA permit” (emphasis added)); see also 

Natural Res. Def. Council, Inc. v. County of Los Angeles, 

725 F.3d 1194, 1205 (9th Cir. 2013) (“Our sole task at this 

point of the case is to determine what Plaintiffs are required 

to show in order to establish liability under the terms of this 

particular NPDES permit.”); see also 33 U.S.C. § 1365(a) 

(authorizing private civil actions against persons who are in 

violation of a “limitation” imposed under the CWA). 

Neither decision addressed the antecedent question of 

whether such a condition, when timely challenged by the 

permittee, is properly included in such a permit in the first 

place. As the EPA conceded at oral argument, the only

circuit court to have addressed that question is the Second 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 61

Circuit, and it held that the condition was invalid for the 

same reasons that I have already explained. See NRDC II v. 

EPA, 808 F.3d at 577–80; see supra section II(A).3 

* * *

For all of these reasons, I would grant San Francisco’s 

petition, vacate the two challenged narrative conditions, and 

remand to the agency.4 

III

The third permit condition challenged here requires San 

Francisco to “update its LTCP by implementing” five 

enumerated tasks that the permit asserts are “based on” the 

CSO Control Policy. Among other things, San Francisco is 

required to undertake a “Consideration of Sensitive Areas” 

and to develop “control alternatives,” including 

infrastructure changes, for “eliminat[ing], relocat[ing], or 

reduc[ing] the magnitude or frequency of discharges to 

sensitive areas.” I agree with San Francisco that this 

condition is contrary to law and must be set aside. See

5 U.S.C. § 706(2)(A). 

A

As noted earlier, the CSO Control Policy is an unusual 

document in that, under § 402(q)(1) of the CWA, it 

effectively has the force of a statute. See 33 U.S.C. 

3 The majority implausibly attempts to distinguish NRDC II on the 

ground that in that case the narrative condition was challenged by a third 

party rather than by the permittee. See Opin. at 32. But regardless of 

which party is seeking greater regulatory clarification, the agency’s 

abdication of its regulatory responsibility is equally indefensible. 

4 I therefore have no occasion to address San Francisco’s further 

argument that the EPA failed to follow its own procedures under 40 

C.F.R. § 122.44(d) when it imposed these two narrative conditions. 
62 CITY & COUNTY OF SAN FRANCISCO V. USEPA

§ 1342(q)(1) (requiring that “[e]ach permit, order, or decree 

issued pursuant to this chapter after December 21, 2000, for 

a discharge from a municipal combined storm and sanitary 

sewer shall conform to the Combined Sewer Overflow 

Control Policy signed by the Administrator on April 11, 

1994”). In my view, the EPA’s direction to San Francisco 

to prepare an updated LTCP does not conform to the CSO 

Control Policy’s limitations on when an amended LTCP may 

be required. It therefore violates § 402(q)(1) of the CWA.

The EPA has previously and repeatedly recognized that 

San Francisco developed an LTCP that, although spanning 

multiple documents over several years, “demonstrated 

compliance with section I.C.1 of the CSO Control Policy” 

and that the City therefore was “not required to complete a 

(new) CSO long-term plan.” See supra at 53–54. But in this 

most recent permit, the EPA has concluded that San 

Francisco must now complete a new LTCP. The question, 

then, is whether the provisions of the CSO Control Policy 

authorize the EPA to require the preparation of a new 

“updated” LTCP in the current circumstances. The answer 

is no.

As the CSO Control Policy acknowledges, the 

preparation of an LTCP involves consideration of alternative 

methods of CSO control that may include substantial and 

costly infrastructure projects. See, e.g., 59 Fed. Reg. at 

18693–94 (requiring consideration of “cost/performance” 

considerations in evaluating options and providing for 

consideration of a “permittee’s financial capability” when 

establishing “[c]onstruction phasing”). It is therefore hardly 

surprising that, in two respects, the Policy expressly 

addresses the circumstances in which the agency may 

require the preparation of an amended LTCP.
CITY & COUNTY OF SAN FRANCISCO V. USEPA 63

First, § I.C.1 of the Policy, which allows substantially 

completed CSO control facilities to be exempted from the 

“initial planning and construction provisions” governing 

LTCPs, states that such permittees remain subject to the 

Policy’s monitoring requirements and that, “[i]f after 

monitoring, it is determined that WQS are not being attained, 

the permittee should be required to submit a revised CSO 

control plan that, once implemented, will attain WQS.” 59 

Fed. Reg. at 18690 (emphasis added). Second, § IV.B.2.g of 

the Policy states that the Phase II permits applicable to 

permittees that have “completed development of the longterm CSO control plan” must include a “reopener clause 

authorizing the NPDES authority to reopen and modify the 

permit upon determination that the CSO controls fail to meet 

WQS or protect designated uses.” Id. at 18696. In the event 

of such a determination, then “the permittee should be 

required to develop, submit and implement, as soon as 

practicable, a revised CSO control plan which contains 

additional controls to meet WQSs and designated uses.” Id. 

(emphasis added). As the plain language of these provisions 

makes clear, there is only one circumstance in which a 

permittee may be required to create a “revised CSO control 

plan,” and that is when the water quality standards 

established to protect the relevant designated uses are not 

being attained.5

When the EPA included a permit condition requiring San 

Francisco to update its LTCP, the EPA explained that it was 

doing so for several enumerated reasons. However, none of 

5 “Designated uses” refers to those “uses of the navigable waters 

involved” that form the basis for the “water quality criteria” for those 

waters. 33 U.S.C. § 1313(c)(2)(A); see generally PUD No. 1, 511 U.S. 

at 714–15. 
64 CITY & COUNTY OF SAN FRANCISCO V. USEPA

those reasons involved (or otherwise referred to) a finding 

that San Francisco’s Oceanside System had caused the 

violation of any applicable water quality standards. Because 

no such determination was made, the Policy’s trigger for 

requiring submission of a revised LTCP has not been met. 

The EPA therefore lacked authority under the Policy to 

impose a condition requiring San Francisco to prepare and 

submit a revised LTCP.

B

The majority pointedly does not contend that water 

quality standards are not being met here. Instead, noting that 

§ IV.B.2.g states that a revised LTCP may be required “upon 

determination that the CSO controls fail to meet WQS or 

protect designated uses,” 59 Fed. Reg. at 18696 (emphasis 

added), the majority holds that this conjunctive phrasing 

gives the EPA authority to require a new LTCP—even 

where water quality standards are being met—if the EPA 

determines that there nonetheless is, in some undefined 

sense, a failure to “protect designated uses.” See Opin. at 

40–41. The majority’s peculiar notion that the protection of 

designated uses will be assessed independently of water 

quality standards makes no sense. Under § 303 of the CWA, 

the applicable “water quality criteria” contained in the 

“water quality standards” are the measuring stick for 

assessing whether “designated uses” are being protected. 33 

U.S.C. § 1313(c)(2)(A); see also PUD No. 1, 511 U.S. at 

714–18. Considered in context, § IV.B.2.g’s reference to 

protecting “designated uses”—which are merely a 

“component[]” of the broader concept of “water quality 

standards,” see Upper Missouri Waterkeeper v. EPA, 15 

F.4th 966, 969–70 (9th Cir. 2021)—thus adds nothing to the 

concept of achieving water quality standards. And because 

the EPA has not determined that water quality standards are 
CITY & COUNTY OF SAN FRANCISCO V. USEPA 65

not being met, § IV.B.2.g did not authorize the EPA to 

require a new LTCP.

The majority also claims that the EPA nonetheless 

possesses such authority by virtue of § I.C.3 of the Policy, 

see Opin. at 39–40, but that is wrong. The relevant language 

cited by the majority states that, “[i]n the case of any ongoing 

or substantially completed CSO control effort, the NPDES 

permit or other enforceable mechanism, as appropriate, 

should be revised to include all appropriate permit 

requirements consistent with Section IV.B. of this Policy.” 

See 59 Fed. Reg. at 18690. To the extent that the majority 

thinks that § I.C.3 establishes a free-floating authority to 

impose permit requirements without regard to § IV.B’s 

provisions governing “NDPES Permit Requirements,” that 

is plainly incorrect. On its face, § I.C.3 merely states that, 

for partially exempted systems (such as San Francisco’s), the 

NPDES permit should include “all appropriate permit 

requirements consistent with Section IV.B. of this Policy.” 

Id. (emphasis added). Any authority conferred by § I.C.3 to 

impose permit conditions therefore remains subject to the 

provisions of § IV.B. And, as I have explained, § IV.B of 

the Policy expressly addresses the issue of preparation of a 

revised LTCP, and it only authorizes requiring such a revised 

plan “upon determination that the CSO controls fail to meet 

WQS or protect designated uses.” Id. at 18696. Because 

that condition is not satisfied here, the EPA’s imposition of 

such a requirement is not “consistent with Section IV.B. of 

this Policy” and is therefore not authorized by § I.C.3. Id. 

The majority consequently errs in concluding that the 

assertedly “outdated” nature of San Francisco’s LTCP is 

“enough, by itself, to support EPA’s conclusion that an 

updated LTCP is needed.” Opin. at 41–42. This holding 

rewrites the CSO Control Policy rather than applies it. 
66 CITY & COUNTY OF SAN FRANCISCO V. USEPA

Perhaps the Policy should have included a broader provision 

that gave the agency greater authority to require a new 

LTCP, and perhaps Congress should have mandated such a 

change before it adopted the 1994 Policy as the statutory 

standard for permits involving combined sewer systems. 

But, as written, the policy allows the agency to order a 

revised LTCP only when a determination is made that the 

permittee’s CSO controls have led to water quality 

standards not being met. As explained, that condition has 

not been established here. Merely labeling San Francisco’s 

LTCP as “outdated” or “inadequate” in some more vague or 

general sense is not enough.

Finally, I note that this conclusion does not leave the 

agency powerless to address specific deficiencies in the 

performance of San Francisco’s system, including with 

respect to protection of sensitive areas. Section IV.B of the 

Policy leaves the agency with ample authority to craft 

targeted conditions addressed to the range of issues covered 

by the provisions of that section. But absent a determination 

that the permittee’s CSO controls have failed to meet water 

quality standards, the agency may not take the much more 

sweeping step of requiring a revision of the LTCP itself. 

Such a condition is “not in accordance with law.” 5 U.S.C. 

§ 706(2)(A).

* * *

Accordingly, I would grant the petition for review on this 

issue as well and would vacate the current permit condition 

requiring San Francisco to prepare an updated LTCP. I 

would do so without prejudice to the agency’s re-evaluation 

of whether particular targeted components of that LTCPrevision condition could be adopted as free-standing 

conditions consistent with § IV.B of the Policy.
CITY & COUNTY OF SAN FRANCISCO V. USEPA 67

IV

For the foregoing reasons, I would grant San Francisco’s 

petition for review, vacate the challenged permit conditions, 

and remand this case to the agency for further consideration. 

I respectfully dissent.