FOR PUBLICATION

UNITED STATES COURT OF APPEALS

FOR THE NINTH CIRCUIT

FOOD & WATER WATCH; SNAKE

RIVER WATERKEEPER, INC.,

Petitioners,

v.

U.S. ENVIRONMENTAL

PROTECTION AGENCY,

Respondent.

No. 20-71554

OPINION

On Petition for Review of an Order of the

Environmental Protection Agency

Argued and Submitted May 6, 2021

Portland, Oregon

Filed September 16, 2021

Before: William A. Fletcher and Michelle T. Friedland,

Circuit Judges, and Frederic Block,* District Judge.

Opinion by Judge W. Fletcher

* The Honorable Frederic Block, United States District Judge for the

Eastern District of New York, sitting by designation.
2 FOOD & WATER WATCH V. USEPA

SUMMARY**

Clean Water Act

The panel granted a petition for review brought by

petitioner environmental organizations challenging a National

Pollutant Discharge Elimination System (“NPDES”) Permit

issued by the Environmental Protection Agency (“EPA”) for

Concentrated Animal Feeding Operations (“CAFOs”) in

Idaho. 

The Clean Water Act prohibits the discharge of any

pollutant by any person from any point source into the

navigable waters of the United States except when the

discharge is authorized by a permit issued under the NPDES. 

CAFOs house, feed, and raise thousands of animals in

confined locations, and they generate animal manure, which

can pose substantial risks to the environment and public

health. Manure is typically stored in lagoons, and animal

waste that leaks from lagoons can reach groundwater that can,

in turn, reach navigable waters. The EPA has regulated

CAFOS since the mid-1970s. The EPA regulates both

production areas and land-application areas of CAFOs.

Production areas include animal confinement areas, manure

storage areas including lagoons, raw materials storage areas,

and waste containment areas. Land-application areas are

fields where manure, litter, and process wastewater are

applied as fertilizer.

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

been prepared by court staff for the convenience of the reader.
FOOD & WATER WATCH V. USEPA 3

The panel held that the petitioners’ challenge was timely. 

The parties agreed that petitioners challenged the Idaho

Permit within 120 days of the issuance. The panel rejected

the EPA’s contention that the Permit largely relied on a 2003

Rule and that the petition was therefore untimely.

The panel agreed with petitioners’ contention that the

Permit lacked sufficient monitoring provisions to ensure

compliance with the Permit’s “zero discharge” requirements

for both production and land-application areas, and therefore,

it was arbitrary, capricious, and an abuse of discretion, and

not in accordance with the law. The statutory and regulatory

framework gives discretion to the EPA in crafting appropriate

monitoring requirements for each NPDES permit, but the

EPA’s discretion is not unlimited. 

Concerning production areas, the panel held the Permit

had sufficient monitoring requirements for above-ground

discharges from production areas. The CAFOs were required

to perform daily inspections, and these mandated inspections

were, in effect, monitoring requirements. The panel deferred

to the EPA’s expertise, and held that these provisions were

sufficient to ensure compliance with the Permit’s zerodischarge effluent limitations from production areas. 

The panel held that the Permit had no monitoring

provisionsfor underground discharges from production areas. 

Without a requirement that CAFOs monitor waste

containment structures for underground discharges, there was

no way to ensure that production areas comply with the

Permit’s zero-discharge requirement. 

Concerning land-application areas, the panel held that

the Idaho Permit flatly prohibited discharges from land-
4 FOOD & WATER WATCH V. USEPA

application areas during dry weather. The Permit, however,

had no monitoring provisions for dryweather discharges from

land-application areas, even though the record before the

EPA showed that such discharges can occur during irrigation

of fertilized CAFO fields. Without a requirement to monitor

runoff from irrigated CAFO fields, there was no way to

ensure that a CAFO is complying with the Permit’s dry

weather no-discharge requirement for land-application areas.

The panel therefore granted the petition and vacated the

permit.

COUNSEL

Tyler Lobdell (argued), Staff Attorney, Food & Water Watch,

Boise, Idaho; Allison M. LaPlante and Danielle Replogle,

Earthrise Law Center, Lewis & Clark Law School, Portland,

Oregon; for Petitioners.

Benjamin J. Grillot (argued), Attorney; Eric Grant, Deputy

Assistant Attorney General; Jonathan D. Brightbill, Principal

DeputyAssistant AttorneyGeneral; Environment andNatural

Resources Division, United States Department of Justice,

Washington, D.C.; Simma Kupchan and CourtneyWeber,

Office of General Counsel and Office of Regional Counsel,

UnitedStatesEnvironmental ProtectionAgency,Washington,

D.C.; for Respondent.
FOOD & WATER WATCH V. USEPA 5

OPINION

W. FLETCHER, Circuit Judge:

The Clean Water Act (“CWA”) prohibits the “discharge

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

into the navigable waters of the United States except when

the discharge is authorized by a permit issued under the

National Pollutant Discharge Elimination System

(“NPDES”). 33 U.S.C. §§ 1311(a), 1342. In May 2020, the

EPA issued a General NPDES Permit for Concentrated

Animal Feeding Operations (“CAFOs”) in Idaho (the “Idaho

Permit” or “Permit”). Final Reissuance of NPDES General

Permit for CAFOs in Idaho, 85 Fed. Reg. 28,624 (May 13,

2020). Two environmental organizations, Food & Water

Watch and Snake River Waterkeeper (“Petitioners”),

challenge the Permit, contending that its issuance was

arbitrary, capricious, and in violation of law because it lacks

sufficientmonitoring provisions to ensure compliance with its

discharge limitations. We agree and grant the petition.

I. Background

Concentrated animal feeding operations house, feed, and

raise thousands of animals in confined locations. NPDES

Permit Regulation and Effluent Limitation Guidelines and

Standards for CAFOs, 68 Fed. Reg. 7,176, 7,179 (Feb. 12,

2003) (codified at 40 C.F.R. Parts 9, 122, 123, and 412)

[hereinafter “the 2003 Rule”]. Nationwide, CAFOs generate

more than 500 million tons of animal manure annually, which

“when improperly managed, can pose substantial risks to the

environment and public health.” Id. In 2008, the EPA

estimated that approximately 75 percent of CAFOs discharge

pollution into waterways. See Revised NPDES Permit
6 FOOD & WATER WATCH V. USEPA

Regulation and Effluent Limitations Guidelines for CAFOs

in Response to the Waterkeeper Decision, 73 Fed. Reg.

70,418, 70,469 (Nov. 20, 2008) (codified at 40 C.F.R. Parts

9, 122, and 412) [hereinafter “the 2008 Rule”]; see also 2003

Rule at 7,181.

CAFOs manage manure by collecting, storing, and

treating it, and applying it to fields as fertilizer. Thomas R.

Head, Local Regulation of Animal Feeding Operations:

Concerns, Limits, and Options for Southeastern States,

6 Env’t Law. 503, 515–16 (2000). Manure is typically stored

in large open-air tanks or anaerobic lagoons. Id. at 515. 

Lagoons pose two serious hazards. First, “even the most

well-managed lagoons usually fill to capacity within just two

or three years.” Id. Unless excess liquid is removed, a

lagoon will overflow. Id. Second, the potential “always

exists that lagoons will fail or rupture and pollute surface

waters or allow waste to seep into groundwater.” Id. “[E]ven

assuming the lagoons were constructed pursuant to [Natural

Resource Conservation Service] standards, these standards

specifically allow for permeability and, thus, the lagoons are

designed to leak.” Cmty. Ass’n for Restoration of the Env’t,

Inc. v. Cow Palace, LLC, 80 F. Supp. 3d 1180, 1223 (E.D.

Wash. 2015). Depending on the character of the soil

surrounding the lagoon, animal waste leaked from lagoons

can reach groundwater that can, in turn, reach navigable

waters. CAFOs typically use animal waste as fertilizer for

their fields. While application of animal waste can be safe,

improper application, rainfall, or irrigation can result in

discharges that reach navigable waters.

Because of the significant environmental threats CAFOs

pose, the EPA has regulated them since the mid-1970s. See
FOOD & WATER WATCH V. USEPA 7

41 Fed. Reg. 11,458 (Mar. 18, 1976); 39 Fed. Reg. 5,704

(Feb. 14, 1974).

A. Statutory Background

The objective of the CWA is to “restore and maintain the

chemical, physical, and biological integrity of the Nation’s

waters.” 33 U.S.C. § 1251(a). To achieve this objective, the

CWA prohibits a point source from discharging pollutants

into the “navigable waters of the United States” without an

NPDES permit. Id. § 1311(a). The CWA defines “discharge

of a pollutant” to mean “any addition of any pollutant to

navigable waters from any point source.” Id. § 1362(12). A

“point source” is “any discernible, confined and discrete

conveyance . . . from which pollutants are or may be

discharged.” Id. § 1362(14).

An NPDES permit limits the amounts and kinds of

pollutants that may be discharged from a point source. See

id. § 1311(a) (making it unlawful for a point source to

discharge a pollutant without first obtaining a permit and

complying with its terms). Every NPDES permit must set

forth “effluent limitations,” that is, certain “restriction[s] . . .

on [the] quantities, rates, and concentrations of chemical,

physical, biological, and other constituents which are

discharged from point sources into navigable waters.” Id.

§§ 1311, 1342, 1362(11); see also S. Fla. Water Mgmt. Dist.

v. Miccosukee Tribe of Indians, 541 U.S. 95, 102 (2004)

(“Generally speaking, the NPDES requires dischargers to

obtain permits that place limits on the type and quantity of

pollutants that can be released into the Nation’s waters.”). 

Specific effluent limitations in individual NPDES permits are

based on general “effluent limitation guidelines” (“ELGs”)

promulgated by the EPA. See EPA v. Cal. ex. rel. State
8 FOOD & WATER WATCH V. USEPA

Water Res. Control Bd., 426 U.S. 200, 205 (1976) (“An

NPDES permit serves to transform generally applicable

effluent limitations and other standards including those based

on water quality into the obligations . . . of the individual

discharger.”).

Section 1362(14) of the CWA lists a CAFO as a point

source. Id. (“The term ‘point source’ means any discernible,

confined and discrete conveyance, including but not limited

to any . . . concentrated animal feeding operation . . . from

which pollutants are or may be discharged.”) (emphasis

added). Section 1362(14) provides that the term point source

“does not include agricultural stormwater discharges and

return flows from irrigated agriculture.” Id.

Because CAFOs are themselves point sources, the EPA

has interpreted the stormwater and irrigation discharge

exceptions as not applying when such discharges are from a

CAFO. For example, the Idaho Permit prohibits dry weather

discharges from a CAFO’s land application area. Discharges

from irrigation return flows are included in the prohibition on

dry-weather discharges. See Idaho Permit at 10 (“No Dry

Weather Discharge. There shall be no dry weather discharge

of manure, litter, or process wastewater to a water of the

United States from a CAFO as a result of the application of

manure, litter or process wastewater . . . . This prohibition

includes discharges . . . through tile drains, ditches or other

conveyances, and irrigation return.” (emphasis added)). 

Further, while the EPA has partially incorporated the

stormwater discharge exception into a CAFO regulation, it

has done so as a matter of regulatory discretion rather than

statutory compulsion. See 40 C.F.R. § 122.23(e) (waiving the

requirement for an NPDES permit for stormwater discharges

from CAFO fields if the CAFO has land applied manure,
FOOD & WATER WATCH V. USEPA 9

litter, or process wastewater in accordance with site-specific

nutrient management practices). But see Waterkeeper

Alliance, Inc. v. U.S. E.P.A, 399 F.3d 486, 507 (2d Cir. 2005);

Concerned Area Residents for the Env’t v. Southview Farm,

34 F.3d 114, 121 (2d Cir. 1994).

B. CAFO Regulations

The EPA regulates both production areas and landapplication areas of CAFOs. Production areas include animal

confinement areas (where animals are confined for feeding or

other purposes), manure storage areas including lagoons

(where manure and other wastes are collected and stored or

treated prior to final disposal), raw materials storage areas

(where materials used in feeding operations are stored), and

waste containment areas (where wastes other than manure are

stored until final use or disposal). 40 C.F.R. § 122.23(b)(8). 

Land-application areas are fields where manure, litter, and

process wastewater are applied as fertilizer. 40 C.F.R.

§ 122.23(b)(3). Both production and land-application areas

are possible sources of discharges of pollutants into navigable

waters. See 2003 Rule at 7,181.

Animal waste contains a number of pollutants. Pollutants

associated with CAFO animal waste include nitrogen and

phosphorus; solids, including manure and animal corpses;

disease-causing viruses and bacteria including E. coli; trace

elements such as arsenic; odorous/volatile compounds such

as methane, hydrogen sulfide, and ammonia; antibiotics;

pesticides; and hormones. See NPDES Permit Regulation

and Effluent Limitations Guidelines and Standards for

CAFOs, 66 Fed. Reg. 2960, 2976–79 (Jan. 12, 2001)

[hereinafter “2001 Proposed Rule”]. Pollutants can reach

surface water and groundwater in a variety of ways, including
10 FOOD & WATER WATCH V. USEPA

overflows and underground leaks from lagoons, and surface

runoff from land-application areas. 68 Fed. Reg. at 7,181.

Recognizing the threats CAFOs pose to water quality, the

EPA began revising its CAFO regulations in 2001. After a

two-year rulemaking process, the EPA promulgated a final

Rule in 2003 (the “2003 Rule”). Among other things, the

2003 Rule required a CAFO either to apply for an NPDES

permit or to demonstrate that it did not have the potential for

discharge. See 2003 Rule at 7,181–82. The 2003 Rule also

required permittees to develop and implement site-specific

nutrient management plans (“NMPs”), and it exempted wet

weather discharges under an exemption for agricultural

stormwater. See 2003 Rule at 7,176. The 2003 Rule did not

establish any general groundwater requirements.

The Second Circuit upheld the 2003 Rule’s incorporation

of the agricultural stormwater exemption into its regulation,

as well as the EPA’s decision to impose groundwater

requirements on a “case-by-case” basis. See Waterkeeper, 

399 F.3d at 497, 507–09, 515. However, the court held that

the Rule was arbitrary, capricious, and contrary to law in

failing to require review by the permitting authority of a

CAFO’s proposed NMP, and in failing to require that the

terms of the NMP be included in an issued permit. Id. at

498–503. The court also held that, in the absence of actual

discharge of a pollutant, the CWA did not authorize the EPA

to impose on CAFOs a general “duty to apply” for an NPDES

permit. Id. at 504–06.

In the wake of Waterkeeper, the EPA revised its CAFO

regulations in 2008 (the “2008 Rule”). In place of the 2003

Rule’s duty to apply, the 2008 Rule required that a CAFO

owner or operator apply for a permit only if the CAFO
FOOD & WATER WATCH V. USEPA 11

“discharge[d] or propose[d] to discharge” pollutants. 2008

Rule at 70,424. The 2008 Rule provided that, in the event of

a discharge, a CAFO could be liable for both the discharge

and for the failure to apply for a permit. Id. at 70,426–27. 

However, a CAFO operator could apply for a “certification”

that the CAFO would not discharge a pollutant. If a certified

CAFO discharged, the CAFO would violate the discharge

prohibition, but would not be liable for failing to apply. The

2008 Rule also required that all NPDES permits include a

requirement that CAFO operators develop and implement an

NMP, and specified that the NMP must be reviewed by the

permitting agency and included in the issued permit. Id. at

70,440–70,457.

In National Pork Producers Council v. U.S. E.P.A.,

635 F.3d 738, 750–53 (5th Cir. 2011), the Fifth Circuit,

elaborating on the analysis of Waterkeeper, held that a noncertified CAFO could be held liable under the CWA for

actual discharges, but could not be held liable for failing to

apply for a permit. In response, the EPA again amended its

regulations. See NPDES Permit Regulation for CAFOs: 

Removal of Vacated Elements in Response to 2011 Court

Decision, 77 Fed. Reg. 44,494 (July 30, 2012).

Under current CAFO regulations, any permit issued to a

CAFO must include a requirement to formulate and

implement an NMP. 40 C.F.R. § 122.42(e)(1). The NMP

must ensure (1) adequate storage of animal waste, (2) proper

management of mortalities, (3) that clean water is diverted

from the production area, (4) that animals do not interact with

clean water; (5) that chemicals and other contaminants are

properly disposed of; (6) that site-specific conservation

practices are used to control runoff; (7) that proper protocols

are used for testing manure, litter, or process wastewater, and
12 FOOD & WATER WATCH V. USEPA

soil; and (8) that manure, litter, or process wastewater is landapplied in a manner that ensures appropriate agricultural

utilization of the nutrients in the manure, litter, or process

wastewater. Id. § 122.42(e)(1)(i)–(viii). Additionally, the

NMP must include a waste “application rate” that

“minimize[s] phosphorus and nitrogen transport from the

field to surface waters.” Id. § 412.4(c)(2).

Current CAFO regulations prohibit the discharge of

manure, litter, or process wastewater pollutants into waters of

the United States from production areas, unless the discharge

is precipitation-related and the production area is designed,

constructed, and maintained to contain all manure, litter, and

process wastewater, including the runoff and the direct

precipitation from a 25-year, 24-hour rainfall event. Id.

§ 412.31(a). The regulations allow wet-weather discharges

of manure, litter, or process wastewater from land-application

areas if the CAFO has identified and implemented

appropriate site-specific measures to minimize discharges. 

Id. §§ 122.23(e), 122.42(e)(1)(vi)–(ix). The regulations do

not address dry-weather discharges from land-application

areas.

C. The Idaho Permit

Idaho is home to a large and growing number of CAFOs,

primarily dairy farms and cattle feed lots in the Snake River

watershed in southern Idaho. Improper management of

CAFO waste has resulted in serious water quality problems

in Idaho. State of Idaho Dep’t of Env’t Quality, Idaho’s 2016

Integrated Report App’x K (2018). Watersheds in CAFOdominated areas have excessive and unsafe levels of E. coli,

fecal coliform, and nutrients, as well as low levels of

dissolved oxygen, which is essential to healthy aquatic life. 
FOOD & WATER WATCH V. USEPA 13

Idaho’s 2016 Integrated Report documented 1,989 miles of

streams and 471 acres of lakes that were contaminated with

E. coli, 239 miles of streams and 55,509 acres of lakes that

were burdened with excessive nutrients, and 920 miles of

streams that contained unsafe levels of fecal coliform. See id.

at 39–40. Many Idaho waterways that pass through CAFOdominated areas are classified as “impaired waters” by the

EPA. Id. App’x H at 89–113 (listing waterways in the

Southwest Basin).

Several Idaho waterways in CAFO-dominated areas show

levels of E. coli that far exceed the Water Quality Criterion

geometric mean of 126 cfu/100 mL. See, e.g., id. at App’x H

at 31 (Hatwai Creek, which borders a CAFO, had elevated

levels of E. coli, nitrogen/nitrate, and phosphorus); see also

id. App’x K at 36 (listing E. coli levels with a geometric

mean of 1,108 cfu/100 mL near Grand View, which houses

one of the world’s largest CAFOs); id. App’x K at 58 (E. coli

levels of 811 cfu/100 mL in Yahoo Creek, which is adjacent

to a number of animal feeding operations); id. App’x K at 59

(E. coli contamination in Pioneer Reservoir). The leading

causes of water impairment in Idaho’s streams are

“combined biota/habitat bioassessments, temperature,

sedimentation/siltation, and Escherichia coli.” State of Idaho

Dep’t of Env’t Quality, Idaho’s 2018/2020 Integrated

Report at xiii (2020). “E. coli in water is a strong indicator

of sewage or animal waste contamination.” U.S. Dep’t

of Interior, Bacteria & E. Coli in Water,

https://www.usgs.gov/special-topic/water-science-school/sc

ience/bacteria-and-e-coli-water?qt-science_center_objects=

0#qt-science_center_objects (last visited Aug. 16, 2021).

On October 23, 2019, the EPA issued for public comment

a draft Permit and Fact Sheet for Idaho CAFOs. 84 Fed. Reg.
14 FOOD & WATER WATCH V. USEPA

56,809. On May 13, 2020, the EPA issued the Idaho Permit,

with an effective date ofJune 15, 2020. 85 Fed. Reg. 28,624.

With one exception, the Idaho Permit forbids discharges

of pollutants from production areas. Pollutants may be

discharged from the production area only if “[t]he production

area is designed, constructed, operated, and maintained to

contain all manure, litter, process wastewater, and the runoff

and direct precipitation from the 25-year, 24-hour storm event

for the location of the CAFO.” CAFOs must perform daily

inspections of all water lines, and must perform weeklyvisual

inspections of all storm water diversion devices, runoff

diversion structures, devices channeling contaminated storm

water, and waste storage structures. All open surface liquid

waste storage structures must have a depth marker that clearly

indicates the minimum capacity necessary to contain the

runoff and direct precipitation of a 25-year, 24-hour rainfall

event. The inspection must note the level in liquid

impoundments as indicated by the depth marker. 

Deficiencies found during inspections must be corrected as

soon as possible.

Also with one exception, the Permit forbids discharges

of pollutants from land-application areas. Wet-weather

discharges are permitted only when manure, litter, and

process wastewater have been applied in accordance with a

site-specific NMP. 40 C.F.R. §§ 122.23(e),

122.42(e)(1)(vi)–(ix). Dry-weather discharges from the landapplication area are flatly prohibited. Idaho Permit at 10.

The Permit requires CAFOs to make records available to

the EPA upon request. Production area records include

documents of all inspections of storage, containment, and

treatment structures; the depth of the manure and process
FOOD & WATER WATCH V. USEPA 15

wastewater in those structures; and inspections of all

stormwater diversions and channel structures. Landapplication area records include documentation of the dates

of manure, litter, or process wastewater application for each

field; the methods of the land application; the results of soil

and manure samples; the dates on which the land-application

equipment was inspected; and that all setback requirements

and conservation practices identified in the NMP were

followed.

The Permit also requires CAFOs to submit annual

reports by March 1 of each year to the EPA and to relevant

state regulatory authorities. If lagoons or other storage

structures have overflowed, operators must analyze the

discharges for various pollutants, including E. coli, nitrogen,

nitrate nitrogen, ammonia nitrogen, phosphorus, and

suspended solids. Reports must describe, inter alia, the

quantity of manure, litter, and process wastewater applied to

fields, as well as the results of manure and soil sample

analyses.

II. Standard of Review

We review general NPDES permits issued by the EPA,

such as the Idaho Permit, under Section 509 of the CWA. 

33 U.S.C. § 1369(b)(1)(F). Under the Administrative

Procedure Act, 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). We must set

aside an agency’s decision if “the agency has relied on factors

which Congress has not intended it to consider, entirely failed

to consider an important aspect of the problem, offered an

explanation for its decision that runs counter to the evidence

before the agency, or is so implausible that it could not be
16 FOOD & WATER WATCH V. USEPA

ascribed to a difference in view or the product of agency

expertise.” Motor Vehicle Mfrs. Ass’n of U.S., Inc. v. State

Farm Mut. Auto. Ins. Co., 463 U.S. 29, 43 (1983). The scope

of our review is narrow. We may not substitute our judgment

for that of the agency. Id. However, the 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. (quoting

Burlington Truck Lines v. United States, 371 U.S. 156, 168

(1962)).

III. Discussion

A. Timeliness of Petition

Petitions for review of the type of NPDES permit at issue

must be filed in a court of appeals within 120 days of the

permit’s issuance. 33 U.S.C. § 1369(b)(1); see also Tex.

Mun. Power Agency v. Adm’r of U.S. E.P.A., 799 F.2d 173,

174 (5th Cir. 1986) (interpreting provision to be

jurisdictional). The parties agree that Petitioners challenged

the Idaho Permit within 120 days of its issuance. However,

the EPA argues that the Permit largely relies on and

incorporates the 2003 Rule, and that Petitioners’ challenge is

therefore untimely.

The EPA relies on the Fifth Circuit’s reasoning in

National Pork Producers, 635 F.3d 738. As described above,

after the Second Circuit’s decision in Waterkeeper, the EPA

revised its earlier 2003 Rule and issued a new final rule in

2008. The 2008 Rule changed the NMP’s procedural

provisions, but did not change the NMP’s substantive

requirements. See 2008 Rule at 70,437 (“[Waterkeeper] did

not affect the substantive requirements for NMPs established
FOOD & WATER WATCH V. USEPA 17

. . . in the 2003 CAFO rule.”). In National Pork Producers,

petitioners argued that the EPA exceeded its authority in the

2008 Rule by requiring all permit applicants to develop and

implement NMP protocols. 635 F.3d at 754. However,

because the 2003 Rule had included this requirement, the

Fifth Circuit deemed the challenge to the 2008 Rule untimely. 

Id.

By contrast, Petitioners do not challenge any part of the

2003 and 2008 Rules. Rather, they challenge the Idaho

Permit, arguing that its requirements for monitoring effluent

discharges are insufficient. This challenge is new and

specific to the Idaho Permit. The novelty of the challenge is

confirmed in the 2003 Rule itself, where the EPA rejected a

proposed provision that would have required discharge

monitoring by CAFOs. The EPA concluded that “factors

affectingwhether such discharges are occurring at CAFOs are

so variable from site to site that a national technology-based

standard is inappropriate.” 2003 Rule at 7,216. In the view

of the EPA, discharge monitoring was “more appropriately

addressed through NPDES permit conditions established by

the permitting authority.” Id. at 7,217; see also Waterkeeper,

399 F.3d at 515 (“Studies do show that variability in

topography, climate, distance to surface water, and geologic

factors influence whether and how pollutant discharges at a

particular site enter surface water via groundwater.”). 

Petitioners’ challenge is therefore timely.

B. Petitioners’ Challenge

An NPDES permit must ensure that discharges comply

with effluent limitations in the permit. As stated by the

Second Circuit in Waterkeeper,
18 FOOD & WATER WATCH V. USEPA

Under the Act, permits authorizing the

discharge of pollutants may issue only where

such permits ensure that every discharge of

pollutants will comply with all applicable

effluent limitations and standards.

Waterkeeper, 399 F.3d at 498 (emphasis in original). 

Petitioners argue that the Permit lacks sufficient monitoring

provisions to ensure compliance with the Permit’s “zero

discharge” requirements, for both production and landapplication areas. They argue that the issuance of the Idaho

Permit is therefore arbitrary, capricious, an abuse of

discretion, and not in accordance with law. For the reasons

that follow, we agree with Petitioners.

1. Discharge Monitoring Under the CWA

To ensure that NPDES permittees comply with the

effluent limitations contained in their permits, the CWA

requires that permits contain “all applicable requirements

[including the effluent limitations statutorily required by

33 U.S.C. § 1311],” and “prescribe conditions . . . to assure

compliance with [all applicable requirements, including

effluent limitations].” 33 U.S.C. § 1342(a)(1)–(2) (emphasis

added). The CWA “demands regulation in fact, not only in

principle.” Waterkeeper, 399 F.3d at 498.

EPA regulations incorporate the monitoring requirements

of the CWA. Under 40 C.F.R. § 122.48(b), permits must

specify “[r]equired monitoring including type, intervals, and

frequency sufficient to yield data which are representative of

the monitored activity including, when appropriate,

continuous monitoring[.]” A permit must “assure compliance

with [the] permit limitations” by including requirements to
FOOD & WATER WATCH V. USEPA 19

monitor the “mass (or other measurement specified in the

permit) for each pollutant limited in the permit; the volume

of effluent discharged from each outfall; other measurements

as appropriate.” 40 C.F.R. § 122.44(i)(1)(i)–(iii); see also

U.S. EPA, NPDES Permit Writers’ Manual at 8-2 (Sept.

2010), https://www.epa.gov/sites/default/files/2015-09/doc

uments/pwm_2010.pdf (“Monitoring is performed to

determine compliance with effluent limitations established in

NPDES permits, establish a basis for enforcement actions,

assess treatment efficiency, characterize effluents and

characterize receiving water.”).

This statutory and regulatory framework gives discretion

to the EPA in crafting appropriate monitoring requirements

for each NPDES permit. However, the EPA’s discretion is

not unlimited. While 40 C.F.R. § 122.44(i) contemplates that

the EPA has discretion to decide which monitoring

requirements to include in an NPDES permit, 40 C.F.R.

§ 122.48(b) specifies that a permit must contain monitoring

provisions “sufficient to yield [representative] data.” See

NLRB v. Brown, 380 U.S. 278, 291 (1965) (“Reviewing

courts are not obliged to stand aside and rubberstamp their

affirmance of administrative decisions that they deem

inconsistent with a statutory mandate or that frustrate the

congressional policyunderlying a statute.”); Buffalo Crushed

Stone, Inc. v. Surface Transp. Bd., 194 F.3d 125, 128–29

(D.C. Cir. 1999) (“[D]eference is not without limit. We will

reject an agency’s interpretation if an alternative reading is

compelled by the regulation’s plain language . . . .” (quotation

marks and citation omitted)).

Our case law confirms that NPDES permits must contain

monitoring provisions sufficient to ensure compliance with

the terms of a permit. For example, in NRDC v. County of
20 FOOD & WATER WATCH V. USEPA

Los Angeles, 725 F.3d 1194, 1207 (9th Cir. 2013), we held

that an NPDES permit is “unlawful if a permittee is not

required to effectively monitor its permit compliance.” We

concluded that the CWA “requires every NPDES permittee

to monitor its discharges into the navigable waters of the

United States in a manner sufficient to determine whether it

is in compliance with the relevant NPDES permit.” Id.

at 1207 (emphasis in original) (citing 33 U.S.C. § 1342(a)(2);

40 C.F.R. § 122.44(i)(1)); see also NRDC v. U.S. EPA,

863 F.2d 1420, 1433–34 (9th Cir. 1988) (finding EPA acted

reasonably by using visual sheen test because it monitored

compliance with the permit’s prohibition on the discharge of

free oil).

Similarly, in NRDC v. U.S. EPA, 808 F.3d 556, 583–84

(2d Cir. 2015), the Second Circuit rejected an NPDES permit

because it lacked monitoring provisions. The EPA had issued

a general permit for the discharge of ballast waters from

vessels. Id. at 583. The permit required vessels to report the

expected dates, times, locations, volumes, and salinities of its

discharges. Id. But the required reports provided little

information on the quality of the ballast water. Id. Because

the reports did not reveal whether a vessel was actually in

compliance with the effluent limitations, the permit violated

the statutory command that NPDES permits include

monitoring sufficient to ensure compliance with applicable

effluent limitations. Id.

Issuance of an NPDES permit is thus arbitrary, capricious,

and contrary to law if the permit fails to include monitoring

provisions that ensure compliance with the permit’s effluent

limitations. As we have previously recognized, “[t]he

NPDES program fundamentally relies on self-monitoring.” 

Sierra Club v. Union Oil Co. of Cal., 813 F.2d 1480, 1491
FOOD & WATER WATCH V. USEPA 21

(9th Cir. 1987), vacated and remanded on other grounds,

485 U.S. 931 (1988), and reinstated and amended by

853 F.2d 667 (9th Cir. 1988). Effective self-monitoring

reveals permit violations, thereby promoting enforcement of

the CWA. See id. at 1492; see also County of Los Angeles,

725 F.3d at 1208 (“The [Act] is viewed by many as the

easiest of the federal environmental statutes to enforce. This

is because persons regulated under the act normally must

report their own compliance and noncompliance to the

regulating agency.” (quotation marks and citation omitted)).

2. Monitoring Under the Idaho Permit

The EPA does not quarrel with the foregoing. It concedes

that a permit must contain sufficient monitoring requirements

to ensure that a CAFO complies with the effluent limitations

in its permit. However, the EPA argues that the Idaho Permit

contains sufficient monitoring requirements to ensure

compliance, and that we must defer to its expertise.

As described above, the Idaho Permit requires CAFO

operators to implement various measures to prevent

discharges from the production and land-application areas. 

Petitioners argue the Permit does not require monitoring that

would ensure detection of unpermitted discharges. We agree

with Petitioners.

a. Production Areas

The Permit has sufficient monitoring requirements for

above-ground discharges from production areas. As noted

above, CAFOs are required to perform daily inspections of

water lines, and weekly inspections of storm water diversion

devices, runoff diversion structures, devices channeling
22 FOOD & WATER WATCH V. USEPA

contaminated storm water, and waste storage containers. 

These mandated inspections are, in effect, monitoring

requirements. We defer to the EPA’s expertise and hold that

these provisions are sufficient to ensure compliance with the

Permit’s zero-discharge effluent limitation from production

areas. For example, the visual inspection of a waste

container’s depth marker ensures that containers maintain

enough space to handle any excess water, thereby preventing

runoff in all but the extreme circumstance of a 25-year, 24-

hour rainfall event. See NRDC, 863 F.2d at 1433–34 (visual

inspections that identifywhether effluent limitation is met are

reasonable).

However, the Permit has no monitoring provisions for

underground discharges from production areas. The record

before the EPA showed that leaky containment structures—

especiallylagoons—are sources of groundwater pollution and

that “groundwater flow is the primary contributor of nitrate

to surface water from agriculture.” See Cow Palace, LLC, 80

F. Supp. 3d at 1223. Despite this, the Idaho Permit has no

monitoring requirement for underground discharges. The

failure of the Permit to require such monitoring is striking,

given the EPA’s conclusion in the 2003 Rule that

requirements in local permits rather than nationally uniform

requirements are the best means to address underground

discharges. In rejecting a proposal that monitoring of

underground discharges be included in the nationwide 2003

Rule, the EPA wrote:

The proposed rule would have imposed

explicit national requirements for certain

CAFOs to address possible discharges to

surface water via ground waters that have a

direct hydrologic connection to surface
FOOD & WATER WATCH V. USEPA 23

waters. These operations would have been

required to sample groundwaters. . . .

In today’s effluent limitation guidelines,

EPA is rejecting establishing requirements

related to discharges to surface water that

occur via ground water with a direct

hydrologic connection.

Pollutant discharges from CAFOs to

surface water via a groundwater pathway are

highly dependent on site-specific variables,

such as topography, climate, distance to

surface water, and geologic factors such as

depth of groundwater, soil porosity and

permeability, and subsurface structure. The

factors affecting whether such discharges are

occurring at CAFOs are so variable from site

to site that a national technology-based

standard is inappropriate.

2003 Rule at 7,216 (emphasis added); see also Waterkeeper,

399 F.3d at 515 (“Studies do show that variability in

topography, climate, distance to surface water, and geologic

factors influence whether and how pollutant discharges at a

particular site enter surface water via groundwater.”).

The CWA requires that the EPA ensure that every

NPDES permittee “monitor its discharges . . . in a manner

sufficient to determine whether it is in compliance with the

relevant NPDES permit.” County of Los Angeles, 725 F.3d

at 1207. With one exception not relevant here, the Idaho

Permit does not allow any discharges from the production

area. Without a requirement that CAFOs monitor waste
24 FOOD & WATER WATCH V. USEPA

containment structures for underground discharges, there is

no way to ensure that production areas comply with the

Permit’s zero-discharge requirement. See Waterkeeper,

399 F.3d at 499 (failure of permit to include any mechanism

for evaluating compliance with effluent limitation was

arbitrary and capricious).

b. Land-Application Areas

As noted above, CAFO regulations allow discharges from

CAFO land-application areas during wet weather, provided

the CAFO has complied with its NMP. See 40 C.F.R.

§ 122.23(e) (“[W]here the manure, litter or process

wastewater has been applied in accordance with site specific

nutrient management practices . . . a precipitation-related

discharge of manure, litter or process wastewater from land

areas under the control of a CAFO is an agricultural

stormwater discharge.”). However, the Idaho Permit flatly

prohibits discharges from land-application areas during dry

weather:

There shall be no dry weather discharge of

manure, litter, or process wastewater to a

water of the United States from a CAFO as a

result of the application of manure, litter or

process wastewater to land areas under the

control of the CAFO. This prohibition

includes discharges to waters of the United

States through tile drains, ditches or other

conveyances, and irrigation return.

The Permit has no monitoring provisions for dry weather

discharges from land-application areas, even though the

record before the EPA showed that such discharges can occur
FOOD & WATER WATCH V. USEPA 25

during irrigation of fertilized CAFO fields. The Permit

assumes that because the NMP requires CAFOs to apply

manure, litter, and process wastewater at the agronomic rates

established by the NMP, irrigation-produced runoff of

pollutants will never occur. There is little in the record to

support that assumption. Without a requirement to monitor

runoff from irrigated CAFO fields, there is no way to ensure

that a CAFO is complying with the Permit’s dry weather nodischarge requirement for land-application areas. See Cnty.

of L.A., 725 F.3d at 1207 (holding that an NPDES permit

must include compliance monitoring measures).

Conclusion

The Idaho Permit forbids underground discharges from

production areas and dry weather discharges from landapplication areas. However, the Permit contains no

monitoring requirements for either kind of discharge. 

Because the Permit does not require monitoring that would

ensure compliance with its effluent limitations, the EPA’s

issuance of the Permit was arbitrary, capricious, and a

violation of law. We grant the petition and vacate the Permit.

Petition GRANTED and Permit VACATED.