Food & Water Watch, Inc. v. Usepa

FOR PUBLICATION

UNITED STATES COURT OF APPEALS
FOR THE NINTH CIRCUIT

FOOD & WATER WATCH; SNAKE No. 20-71554
RIVER WATERKEEPER, INC.,
Petitioners,
OPINION
v.

U.S. ENVIRONMENTAL
PROTECTION AGENCY,
Respondent.

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 zero-
discharge effluent limitations from production areas.

The panel held that the Permit had no monitoring
provisions for 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 dry weather 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
Deputy Assistant Attorney General; Environment and Natural
Resources Division, United States Department of Justice,
Washington, D.C.; Simma Kupchan and CourtneyWeber,
Office of General Counsel and Office of Regional Counsel,
United States Environmental Protection Agency, 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
sufficient monitoring 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 land-
application 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 non-
certified 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 land-
applied 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 CAFO-
dominated 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 CAFO-
dominated 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 of June 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 weekly visual
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 land-
application 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. Land-
application 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
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. 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 land-
application 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 policy underlying 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 identify whether 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—
especially lagoons—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 no-
discharge 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 land-
application 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.