F OR P UBLICATION



### UNIT E D ST AT E S CO URT O F APPE AL S FO R T H E NINT H CIRCUIT

F O O D & W A T E R W A T C H ; S N A K E R I V E R W A T E R

K E E P E R , I N C

. , Petitioners
,

v.

U.S. E N V I R O N M E N T A L P R O T E C T I O N A G E

N C Y , Respondent. No. 20-71554

OPI NI ON

O n Petition for Review of an Order of the Environmental Protection Ag ency
Arg ued and Submitted May 6, 2021 Portland, Oreg on

F iled September 16, 2021

B efore: W illiam A. F letcher and Michelle T. F riedland, Circuit J udg es, and F rederic B lock, * District J udg e.

Opinion by

J udg e W

. F letcher

* T h e Ho n o rab le Fred eric B lo ck
, Un i ted S tates District J u d g e f o r th e Eastern District o f

New Yo rk , sittin g b y

d esig n atio n

.F O O D & W A T E R W A T C H V

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SUMMARY * *

C lean Water Act

T h e panel g ranted a petition for review broug ht b y petitioner environmenta l o r g a n i za t i o n s c h a l l e n g i n g a National Pollutant Discharg e Elimination Sy stem (“NPDES”) P ermit issued by the Environmental Protection Ag ency ( “EPA”) for Concentrated An i m al F eeding Operations (“CAF Os”) in I daho.

The C l e a n W ater Act prohibits the discharg e of any pollutant b y any pe r son from any p oint source into the navig able w aters of the U n i t e d States e x cept when the discharg e is authoriz ed by a permit issued under the NPDES. C AF O s house, feed, and raise thousands of animal s i n confined locations, and they g enerate animal manure, which

can pose substantial r isks to the environment a n d public health. Manure is ty

pically stored in lag oons, and animal
waste that leaks from lag oons can reach g roundwater that can, in turn, r e a c h navig able waters. T h e EPA has r eg ulated CAF O S since the mid-1970s. The EPA reg ulates both
p r o d uction a

reas and land-application areas of CAF Os. Production areas include animal confinement a reas, m anure storag e areas including lag oons, raw materials storag e areas, and waste containment areas. L and-application areas a re fields where manure, litter, and process wastewater a re applied as fertiliz er.

** T h is su m m ary co n stitu

t es n o p art o f th e o p in io n o f th e co u rt. It h as b een p rep ared b y

co u rt staf

f f o r th e co n v en i en ce o f

th e read er.F O O D & W A T E R W A T C H V

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The panel held that the petitioners’ challeng e was timely

. The parties ag reed that petitioners challenged the I daho Permit within 120 day s o f the i s s uance. The panel rejected the EPA’s contention that the Permit larg ely relied o n a 2003 Rule and that the petition was therefore untimely

.

The panel ag reed with p etitioners’ contention that the Permit l acked sufficient monitoring provisions to ensure compliance with the Permit’s “z ero discharg e” requirements for both production and land-application areas, and therefore, it was arbitrary
, capricious, and an abuse of dis c r e t i o n , a nd
not in a ccordance with the law. The statutory and reg ulatory framework g ives discretion to the EPA in crafting appropriate monitoring r e q u irements 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-g r ound discharg es from production areas. The CAF O s were r equired
to p erform daily inspections, and these mandated inspections
were, in effect, monitoring requirements. The panel deferred
to the EPA’s e x p ertise, and held t hat these provisions were suffici e n t to ensure compliance with the Permit’s z erodischarg e effluent limitations from production areas.

The panel held that the Permit had no monitoring provisi o n s f

o r u nderg round discharg es from production areas. W ithout a requirement that CAF Os monitor waste containment structures for underg round d ischarg e s, there was

no way to ensure that production areas comply w ith the Permit’s z ero-discharg e requirement.

Concerning land-application a r eas, th e panel held that the I daho Permit flatly proh i b i t ed discharg es f rom land-F O O D & W A T E R W A T C H V

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application a

reas during dry weather. The Permit, however, had no monitoring provisions f or dry weather discharg es from land-application areas , e ven thoug h the record before the EPA showed that such d ischarg es can occur during irrig ation of fertiliz e d CAF O fields. W ithout a requirement to monitor runoff fro m i r r i g ated CAF O fields, there was no way to

e n s u r e that a CAF O is comply ing with the Permit’s dr y weather no-discharg e requirement for land-application areas.

The panel therefore g ranted the p etition and vacated the permit.

COUNSEL

Ty ler L obdell (arg

u e d ), Staff Attorney
, F ood & W ater W atch, B oise, I daho; Allison M. L aPlante and Danielle Replog le, Earthrise L aw Center, L ewis & Clark L a w School, Portland, Oreg on; for Petitioners.

B enjamin J

. G rillot (arg

ued), Attorney ; Eric G r a n t, Deputy Assistant Attorney General; J onathan D. B rig htbill, Principal Deputy Assistant Attorney General; Environm e n t a n d Natural Resou rc e s Division, United States Department of J ustice, W a shing ton, D.C.; Simma Kupchan an d Courtney W e ber, Office of General Counsel and O ffice of Reg ional Cou n sel, U n i t e d S t a

t e s E nvironmental Protection A g e n c y , Wa s h i n g t o n , D.C.; for Respondent.F O O D & W A T E R W A T C H V

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OP INION

W

. F L ETCHER, Circuit J udg e:

The Clean W at e r Act (“CW A”) prohibits the “discharg e of any pollutant” by “any p er s o n” from any “point source” into the navig able w aters of the United States ex ce p t when the di s charg e is authoriz ed by a permit issued under the N a t i o n a l P o l l u t a n t D i s c h a r g e E l i m i n a t i o n S ys t e m (“NPDES”). 33 U.S.C. §§ 1311(a), 1342. I n May 2020, the EPA issued a Gene r al N PDES Permit for Concentrated Animal F eeding Operations ( “CAF Os”) in I daho (the “I daho Permit” o r “Permit”). F inal Reissuance of NPDES General Permit f or CAF Os i n I daho, 85 F ed. Reg

. 28,624 ( May 13, 2020). Two e nviro n m e n t al org aniz ations, F ood & W ater W a tch and Snake River W aterkeeper (“Petiti o n ers”), challeng e the Permit, contending t h at its issuance was arbitrary , capricious, and in v iolation o f law because it lacks

s u f f i c i e n t m o n i toring provisions to ensure compliance with its discharg e limitations. W e ag ree and g rant the petition.

I . B ackg round

Concentrated animal feeding operations house, feed, a nd raise thousands of animals in c onfined locations. NPDES Perm i t Reg ulation and E ffluent L imitation Guidelines a nd Standar d s f

o r CAF Os, 68 F ed. Reg

. 7,176, 7,179 (F eb. 12, 2003) (cod i f

i e d a t 40 C.F .R. Parts 9
, 122, 123, and 412) [ hereinafter “the 2003 Rule”]

. Nationwide, CAF Os g enerate

more than 500 million tons of animal manure annually
, which “when improperly manag ed, can pose substantial risks to the environment a

nd public health. ” Id. I n 2008, the EPA estimated that approx imately 7 5 p ercent of CAF Os discharg e pollution into w a t erway s. See Revised NPDES PermitF O O D & W A T E R W A T C H V

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Reg ulation and E ffluent L imitations Guide l i nes for CAF O s in Resp onse to the W

aterkeeper D ecision, 7 3 F ed. Reg

. 70,418, 7 0,469 (Nov. 20, 2 008) ( c o d i f ied at 40 C.F .R. Parts 9, 122, a nd 412) [ hereinafter “the 2008 Rule”] ; see also 2003 Rule at 7,181.

CAF Os manag e manure by coll ec t ing
, storing
, a nd treating it, and apply ing it to fields a s f e rtiliz er. Thomas R. Head, L ocal Regulation of Animal Feeding Operations: Concerns, Limits, and Options for Sout h e a stern States
, 6 Env’t L aw. 503, 5 15–16 (2000). Manure is ty pically stored in larg e open-air tanks or anaerobic lag oons. Id. at 515. L ag oons pose two seri o u s haz a rds. F irst, “even the most well-manag e d lag oons usually fill to capacity within just two

or three y ears.” Id. Unless ex c e s s l i q u i d is removed, a lag oon will overflow. I d. Second, the potential “alway s

ex ists that lag oons will fail or rupture and pollute surface
waters or allow waste to seep into g roundwater.” Id. “[ E] v en assuming the lag oons were constructed p ursuant to [ Natural Resource Conservation Service] standard s , these standards specifically allow f

or permeability and, thus, the lag oons a re desig ned to leak.” Cmty. Ass’n for Restoration of the Env’t, I n c. v. Cow Palace, LLC
, 80 F

. Supp. 3 d 1180, 1223 (E

. D

. W a sh. 2015). D e pending on the c h aracter of the soil

s u r r o u nding the lag oon, animal waste leaked from lag oons

can r e ac h g roundwater that can, in turn, reach n avig able
waters. CAF Os ty

p i c ally u se animal waste a s fertiliz er for their fields. W hile application o f animal waste can be safe, improper app l i cation, r ainfall, or irrig ation can result in discharg es that reach navig able waters.

B e cause of the sig nificant e nvironmental threats CAF O s pose, the EPA has reg u lated them since the mid-1970s. SeeF O O D & W A T E R W A T C H V

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41 F ed. Reg

. 11,458 ( Mar. 18, 1976); 39 F ed. Reg

. 5,704 (F eb. 14, 1974).

A. Statutory B ackg round

The objective of the CW A is to “restore and maintain the chemical, phy sical, and b iolog ical integ rity of the Nation’s waters.” 3 3 U .S.C. § 1251(a). To achieve this objective, the CW A prohi b its a point source from discharg ing pollutants into the “navig able waters o f the United States” without an NPDES permit. Id. § 1311(a). The CW A defines “discharg e of a pollutant” to mean “any ad d i t i o n of any pollutant to navig able waters from any point source.” Id. § 1362(12). A “point source” is “any d iscernibl e , co nfined and discrete
convey ance

. . . fr o m wh i c h pollutants a re or may be discharg ed.” Id. § 1362(14).

An NPDES permit limits the amounts and kinds o f pollutants that may be discharg ed from a p o i n t source. See id. § 1 311(a) (making it unlawful for a point source to discharg e a pollutant w ithout first o b t a i n ing a p ermit a nd

co m p l y i n g with its terms). Every NPDES permit must set forth “effluent limitations,” that is, certain “restriction[ s]

. . . on [ the] q

uantities, rates, and concentrations of chemical, phy sical, biolog ical, and other con s t ituents which a re discharg ed from point sources in t o navig able waters.” Id. §§ 1311, 1342, 1362(11); see also S. Fla. W ater Mgmt. Dist.

v. Miccosukee Tribe of Indians
, 5 4 1 U.S. 95, 1 0 2 (2004) (“Generally speaking
, the NPDES requi r e s discharg e rs to obtain permits that place limits on the ty pe and qua n t i t y o f pollutants that can be released into the Nation’s w aters.”). Specific effluent limitations in individual NPDES permits a re based on g e neral “effluent limitation g uidelines” (“EL Gs”) promulga t e d by the EPA. See EPA v. Cal. ex. rel. StateF O O D & W A T E R W A T C H V

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W ater Res. Control Bd.
, 426 U.S. 200, 205 (1976) (“ A n NPDES p ermit serves to transform g enerally applicable effluent limitations and other standards including those based

on water quality into the oblig a tions

. . . of the individual discharg er.”).

Section 1362(14) o f the CW A lists a CAF O as a point

source. Id. (“The term ‘point source’ means any discernible, confined and d i s c r ete convey ance, including but not limited
t o any

. . . c oncentrated animal feeding operation

. . . f r o m which pollutants are or may be discharg ed.”) ( e m p h asis added). Section 1 362(14) provides that the term point source “does not include ag r i c ultural stormwater discharg es a nd return flows from irrig ated ag r iculture.” Id.

B e cause CAF Os are themselves point s o u r ces, the EPA has interpreted the stormwater a n d irrig ation discharg e

ex c e ptions a s n ot apply ing when such d is c h a rg e s a re from a CAF O. F or ex ample, the I daho Permit prohibits dry weather discharg es from a CAF O’s land a pplication area. Discharg e s from irrig ation return flows are included in the prohibition on dry -weather discharg es. See I daho Permit at 10 ( “ No Dry W eather Discharge

. There shall be n o dry weather discharg e of manure, litter, or process w ast ewater to a water of the United States from a CAFO a s a result of the application o f

manur e , litter or process wastewater

. . . . This prohibition includes discharg es

. . . throug h tile drains, di t c h es or other
convey ances, and irrigation retu r n .” (emphasis added)). F urther, while the EPA has partially i n c o rporated the
stormwater discharg e e x ception into a CAF O reg u la t i o n , it has done so as a matter of reg ulatory discretio n r a ther than statutory compulsion. S

ee 40 C.F .R. § 122.23(e) (waiving the requirement for a

n NPDES permit for stormwater d ischarg e s from CAF O fields if the CAF O has land applied manure,F O O D & W A T E R W A T C H V

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litter, or p r ocess wastewater in accordance with site-specific nutrient manag ement practices). Bu t see W aterkeeper Alliance, Inc. v. U.S. E.P.A
, 399 F .3d 486, 507 (2d Cir. 2 005); Concerned Area Residents for the Env’t v. Southview Farm
, 34 F .3d 114, 121 (2d Cir. 1994).

B . CAF O Reg ulations

The EPA reg u lates b o th product i o n areas and landapplication areas of CAF Os. Production areas include animal confinement a

reas (where animals are c onfined f or feeding o r other p u r p o ses), manure storag e a reas including lag oons (where manure and other wastes are collected an d s tored o r treated prior to final dispo s al), raw materials storag e areas (where materials used in feeding operations are stored), a nd
waste containment areas ( where w astes o ther than manure a re stored until f

inal use o r disposal). 40 C.F .R. § 1 2 2.23(b)(8). L and-application a

reas are fields where manur e , litter, a nd
process wastewater are applied as ferti l i z e r

. 40 C.F .R. § 122.23(b)(3). B oth p roduction a nd la n d

- a pplication areas

are possible sources of discharg es of pollutants into n avig able
waters. See 2003 Rule at 7,181.

Animal waste contains a number of pollutants. Pollutants associated with CAF O a n imal waste i n c l ude nitrog en a nd phos p h o r us; solids, including manure and animal corpses; d isease-causing viruses and bacteria including E. coli ; tra c e elements such as arsenic; odorous/volatile comp ounds such

as methane, hy drog en sulfide, and amm onia; a ntibiotics; pesticides; and h o rmones. See NPDES Permit Reg ulation and E f fluent L imitations Guidelines and Standards for CAF Os, 66 F ed. Reg

. 2960, 297 6

– 7 9 ( J an. 12, 2 001) [ hereinafter “2001 Proposed Rule”]

. Pollutants can reach surface water and g roundwater in a variety of way s, includingF O O D & W A T E R W A T C H V

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overflows and underground leaks from lag oons, a nd surface runoff from land-application areas. 68 F ed. Reg . at 7,181.

Recog niz ing the threats CAF Os pose to water quality
, the EPA beg an revising its C A F O reg ulations in 2001. After a t w o

- y ear rulemaking process, the EPA promulg ated a final Rul e i n 2 0 03 (the “2003 Rule”). Among other thing s, the 2003 Rule required a CAFO ei t h e r to apply for an NPDES permit or to demonstrate that it did not have the potential for discharg e. See 2003 Rule at 7,181–82. The 2003 R u le also required p ermittees to develop a nd implement site-specific nutrien t m a nag ement plans (“NMPs”), a nd it ex empted w et weath e r discharg es under an ex emption f or ag ricultural
stormwater. See 2003 Rule at 7,176. The 2003 Rule did not establish any g eneral g roundwater requirements.

The Second Circuit upheld the 2 003 Rule’s incorporation

o f the ag ricultural stormwater ex emption into its reg ulation,

as w ell a s the EPA’s de c i s ion to impose g roundwater requirements on a “case-by -case” basis. See W

aterkeeper
, 399 F .3d at 497, 507–09, 5 15. However, the court held that the Rule was arbitrary
, capricious, and contrary to law in failing to require review by the pe r mitting a uthority of a CAF O’s propo s e d N M P, and in failing to require that the
terms o f the NMP be included in an issued pe r m i t

. I d

. at 498–503. Th e court also held that, in the absence of actual discharg e of a pollutant, the CW A did not authoriz e the EPA
to impose on CAF Os a g eneral “duty to apply ” for an NPDES permit. Id. at 504–06.

I n the wake of W

aterkeeper
, the EPA rev ised its CAF O
reg ulations in 2008 (the “2008 Rule”). I n p l a c e o f the 2003 Rule’s duty to apply
, the 2 0 0 8 R u le required that a CAF O

owner or operator apply for a p ermit only if the CAF OF O O D & W A T E R W A T C H V

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“discharg e[ d] or propose[ d] to discharg e” p o llutants. 2008 Rule at 70,424. The 2 008 Rule p rovided that, in the event o f

a discharg e , a CAF O c ould be liable for both the discha r ge and f or the failure to apply for a pe rmit. Id. at 70,426–27. However, a CAF O operator could apply for a “certification” that the CAF O would not discharg e a pollutant. I f a c ertified C A FO discharg ed, the CAF O would violate the discharge prohibition, but would not be liable for failing to a pply

. The 2008 Rule a l s o r equired that all NPDES permits include a requirement that CAF O operators develop and implement an NM P
, and specified that the N MP must be reviewed by the permitting ag ency and i ncluded in the issued permit. Id. at 70,440–70,457.

I n National Pork Producers C o uncil v. U.S. E.P.A.
, 635 F .3d 738, 750–53 (5th Cir. 2 0 1 1 )
, the F ifth Circuit,

e laborating o n the analy sis of W aterkeeper
, held that a n o n

certified CAF O could be held liable under the C W A for

a c t u al discharg es, but could not be held liable for failing to apply for a permit. I n r esponse, the E P A ag ain a mended its
reg ulations. See NPDES Permit Re g ulation for CAF Os: Removal of V acated Elements i n Response to 2011 Court Decision, 77 F ed. Reg

. 44,494 (J uly 30, 2012).

Under current CAF O reg ulations, any p ermit issued to a CAF O must in c l u d e a requirement to formulate a nd implement an NMP. 4 0 C .F .R. § 122.42(e)(1). The NMP must ensure (1) adequate storag e of animal waste, (2) proper manag ement of mortalities, (3) that clean water is diverted from the production a

rea, (4) that animals do not interact with clean water; (5) that chemi cals and other contaminants a re properly disposed of; (6) that site-specific conser v a t ion practices are used to control r unoff; ( 7) that proper protocols

are used for testing manure, litter, or process wastewater, a ndF O O D & W A T E R W A T C H V

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soil; and (8) that manure, litter, or process wastewater is landapplied in a manner t hat ensures appropriate ag ricultural utiliz ation o f the nu t r ients in the manure, litter, or process wastewater. Id. § 122.42(e)(1)(i)–(v i i i ). Additionally
, the N MP must include a waste “application rate” t h at “minimiz e [ s] phosphorus and n itr o ge n transport f rom the field to surface waters.” Id. § 412.4(c)(2).

Current CAF O reg u lations prohibit the d ischarg e o f
manure, litter, or process w astewater pollutants into waters o f the U nited States from production areas, unless the discharg e is precipitation-related and the productio n a rea is desig ned, constructed, and maintained to contain all manure, litter, a nd
process wastewate r , including the runoff and the direct precipitation from a 2 5-y ear, 2 4-hour rainf a ll event. Id. § 412.31(a). The reg ulations a llow wet-we a t h e r d ischarg e s of manure, litter, or p rocess wastewater from land-application

area s i f the CAF O h as identified and implemented appropriate site-specific measures to m inimiz e d ischarg es. Id. § § 1 2 2.23(e), 122.42(e)(1)(vi)–(ix ). T he reg u lations do
not address dry -weather discharg es from land- application

areas.

C. The I daho Permit

I daho is home to a larg e and g r o wing number of CAF Os, primarily d airy farms and c a ttle feed lots in the Snake River
waters h e d i n southern I daho. I mproper manag ement o f CAF O waste has resulted in serious water quality p r o blems in I daho. State of I daho D ep’t of Env’t Quality
, I daho’s 2016 I nteg rated Report App’x K (2018). W atersheds in CAF Odominated areas have ex c e ssive and unsafe levels of E. coli
, fe c al coliform, and nutrients, as well as low levels o f dissolved o x y g en, which is essential to healthy aquatic life.F O O D & W A T E R W A T C H V

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I daho’s 2016 I nteg rated Report documented 1,989 miles o f

s t r e a ms and 471 acres of lakes that were contaminated wi t h E. coli
, 2 3 9 miles of streams a nd 55,509 acres o f lakes that

were burdened w ith ex cessive nutrients, and 920 mi l es o f
streams that contained unsafe levels o f fecal coliform. See id.
at 39–40. Many I daho waterway s that pass throug h CAF Odominated areas are classified as “impaired waters” b y t h e EPA. Id

. App’x H at 89–113 ( listing waterway s in the Southwest B asin).

Several I d a

ho waterway s in C AF O -dominated areas show levels of E

. coli that far ex ceed the W ate r Q u a l ity Criterion
g eometric mean of 126 cfu/100 mL

. See, e.g. , id. at App’x H
at 31 (Hatwai Cre ek, which borders a CAF O, h ad e levated levels of E. coli
, nitrog en/nitrate, an d p h osphorus); see also id. App’x K a t 36 (listing E

. coli levels w i t h a g eometric

mean of 1,108 cfu/100 mL near Gra n d V iew, which houses

one of the world’s larg est CAF Os); id. App’x K at 58 ( E. coli levels o f 811 cfu/100 mL in Yahoo Creek, which is a djacent
to a number of animal feeding operations); id. App’x K at 59 ( E

. c oli c ontamination in Pioneer Res e rvoir). The leading

causes of water impairment in I daho’s streams a re “co m b i n e d b i o t a / h a b i t a t b i o assessments, temperature, sedimentation/siltation, and E scherichia coli .” State of I daho Dep’t o f Env’t Quality
, I d a h o’s 2 018/2020 I n teg rated Report at x iii ( 2020). “ E. coli in water is a strong indicator of sewag e or animal w a s t e contamination.” U.S. Dep’t

o f I n t e r i o r , B a c t e r i a & E

. C o l i i n W a t e r , https://www.usg s.g ov/special- t o p i c / w a t e r-science-school/sc ience/bacteria-and-e-coli-wa t e r ? q t

- s c i e n c e

_ c en t e r

_ o bjects= 0#qt-science_center_objects (last visited Aug . 16, 2021).

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

a draft Permit and F act Sheet for I daho CAF Os. 84 F ed. Reg

.F O O D & W A T E R W A T C H V

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56,809. On May 13, 2020, the EPA issued the I d aho Permit, with an effective date o f J une 15, 2020. 85 F ed. Reg

. 28,624.

W ith one ex ception, the I daho Permit forbids discharg e s of pollutants from producti o n areas. Pollutants may be discharg ed from the production area o nly if “[ t] he production

area is desig ned, constructed, operated, and mainta i n e d to contain all manure, litter, process w astewater, and the runoff and direct p recipitation from the 25-y ear, 24-hour storm event for the location o f the CAF O .” CAF Os must perform da i l y 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 w aste storag e str u c t u r es. All open surface liquid
waste storag e structures must have a depth marker that clearly indicates the minimum capac i t y necessary to contain the runoff and d irect p r ecipitation of a 25-y ear, 24-hour rainfall

e v e nt. The inspection must note the level in liquid impoundments as indic a t e d b y the depth marker. Deficiencies f

ound during inspections must be corrected a s soon as possible.

Also w ith one ex cepti o n, the Permit forbids d ischarg e s of pollutant s f

r o m land-application areas. W e t-weather discharg es are permitted only w hen m a n ure, litter, a nd
process wastewater have been applied in accor d a n ce with a

s i t e

- s p e c i f

i c N M P

. 4 0 C

. F

. R

. § § 1 2 2

. 2 3 ( e )
, 122.42(e)(1)(vi)–(ix )

. D ry -weather discharg es from the landapplication area are flatly prohibited. I daho Permit at 10.

The Permit requires CAF Os to make records available to the E PA u

pon request. Product ion a rea records include documents of all inspections of storag e, containment
, a nd
treatment structures; the d epth of the manure and pro c e s sF O O D & W A T E R W A T C H V

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wastewater in those structure s; and inspections of all
stormwater diversions and channe l s t ructures. L andapplication area records includ e d ocumentation of the dates of manure, litter, or p rocess wastewater application for e ach field; the methods of the land applicat i o n ; t h e results of soil and manure samples; the dates on w hich the land-application equipment was inspected; and that a ll setback requi rements and conservation practices identified in the NMP were followed.

The Permit also r e q u ires CAF Os to submit annual reports by March 1 of each y ear to the E PA and t o relevant
state reg ulatory authorities. I f lag oons or o t h e r storag e structures h ave overflowed, operators must analy ze the discharg es f

or various p ollutants, including E. coli
, nitrog en, nitrate nitrog en, ammonia nitrog e n, p h osphorus, a nd suspended solids. Reports must desc r ibe, inter alia
, the quantity of manure, litter, and process wastewater applied to fields, as well as the results of manur e a n d s oil sample analy ses.

I I . Standard of Review

W e r eview g eneral NPDES permits issued by the EPA, such as the I daho P e rmit, under Section 509 of the CW A

. 33 U.S.C. § 1369(b)(1)(F ). Under th e A dministrative Procedure Act, we must set aside an ag ency ’s d ecision if it is “arbitrary
, capricious, a

n abuse of discretion, or otherwise not in a c cordance with law.” 5 U.S.C. § 706(2)(A). W e must set aside an ag ency ’s decision if “the ag ency has relied on f actors which Cong ress has not intended it to consider, entirely failed
to consider an important a s pect of the problem, offered an

ex p lanation for its decision that runs counter to the evidence before the a g ency , or is so impl a u sible that it could not beF O O D & W A T E R W A T C H V

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ascribed to a difference in view or the product of ag ency

ex p ertise.” Motor Vehicle Mfrs. Ass’n o f U.S., Inc

. v

. S t a te Farm Mut. A uto. Ins. Co.
, 463 U.S. 29, 43 (1983). The scope of our review is narrow. W e may not substitute our judg ment for t h a t o f the ag ency

. Id. H owever, the ag ency must “ex a mine the relevant data” a n d “articulate a satisf

a c tory

ex p lanation for its action including a ‘rational connection between the facts found and the choice made.’” Id. ( quoting Burlington Truck Lines v. U nited S tates , 371 U.S. 1 5 6
, 168 (1962)).

I I I

. Discussion

A. Timeliness of Petition

Petitions f

or review of the ty

p e of NPDES permit at issue
must be filed in a court of appeals withi n 1 2 0 d ay s of the permit’s issuance. 33 U.S.C. § 1369( b )(1); see also Tex. Mun. Power A gency v. Adm’r of U.S. E.P. A

. , 7 99 F .2d 173, 174 (5th Cir. 1986) ( i n t erpreting provision to be jurisdictional). The parties ag ree that Petitioners challeng ed the I daho Permit within 120 day s o f i t s i ssuance. However, the EPA arg ues that the Permit larg ely relies on a nd incorporates the 2003 Rule, and that Petitioners’ challeng e is therefore untimely

.

The EPA r elies o n the F ifth Circuit’s reasoning in National Pork Producers
, 635 F

. 3d 738. As described above, after the Second Circuit’s decision in W aterkeeper , the EPA revised its e arlier 2003 Rule and issued a new f inal rule in 2008. T he 2 0 0 8 R u le chang ed the NMP’s procedural
p r o visions, but did n ot chang e the NMP’s substanti v e requirements. See 2008 Rule at 70,437 (“[ W aterkeeper ] did
not affect the substantive requirements for NMPs e stablishedF O O D & W A T E R W A T C H V

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. . . in the 2003 CAF O rule.”). I n National Pork Producers
, petitioners arg ued that the EPA ex ceeded its authority in the 2008 Rule by requiring a ll perm i t applicants to develop a nd im p l e ment NMP protocols. 635 F .3d at 754. However, because the 2003 Rule had included this requirement, the F ifth Circuit deemed the challeng e to the 2008 Rule untimely

. Id.

B y c ontrast, Petitioners do n o t c halleng e any part o f the 2003 and 2008 Rules. Rather, they cha lleng e the I daho Permit, arg u ing that its requirements for monitoring effluent dischar ge s are insufficient. This c halleng e is new a nd specific to the I daho Permit. The novelty of the challeng e is

c onfirmed in the 2003 Rule itself, where the EPA r ejected a proposed provision that would have required discharg e monitoring b y CAF Os. The E P A c o ncluded that “factors affecting whether such discharg es are occurring at CAF Os a re so variable from site to site that a national technolog y -based standard is inappropriate.” 2003 Rule at 7,216. I n the view of the EPA, discharg e monitoring was “more a p p r opriately addressed throug h NPDES permit conditions est a b l i shed b y the p ermitting authority .” Id. at 7,217; see also W aterkeeper
, 399 F

. 3d at 515 (“Studies do show tha t v a r i ability in topog raphy
, climate, distance to surface water, and g eolog ic factors influence whethe r a n d how pollutant discharg es a t a particular site enter surface water v ia g roundwater.”). Petitioners’ challeng e is therefore timely

.

B

. Petitioners’ Challeng e

An N PDES p ermit m u s t e nsure that discharg es comply with effluent limitations i n the permit. As stated by the Second Circuit in W

aterkeeper
,F O O D & W A T E R W A T C H V

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18

U n d er the A ct, permits authoriz ing the discharg e of pollutants may issue only where such permits ensure that ev e r y discharg e o f pollutants wil l c omply with all applicable effluent limitations and standards.

W aterkeeper
, 399 F .3d at 498 ( empha s i s in orig inal). Petitione r s a rg ue that the Permit lacks sufficient monitoring provisions to ensure c o mpliance with the Permit ’s “z ero discharg e” requirements, for both prod u c t i on a nd landapplication a

reas. T hey arg ue that the issuance o f t h e I daho P er m it is therefore arbitrary
, c a pricious, an a

buse o f discretion, and n o t i n accordance with law. F or the reasons that follow, we ag ree with Petitioners.

1. Discharg e Monitoring Under the CW A

To ensure that NPDES permittees comply with the effluent limitations c o ntained in their permits, the CW A requires that p ermits contain “all app l icable requirements [ including the effluent limitations s tatutorily required b y 33 U.S.C. § 1311] ,” and “prescrib e c o n d itions

. . . to a ssure compliance with [all applicable requirements, including effluent limitations] .” 33 U.S.C. § 1342(a)(1)–(2) (emphasis added). The CW A “demands reg ulation in fact
, n o t o n ly in principle.” W

aterkeeper , 399 F .3d at 498.

EPA reg ulations incorporate the monitoring requirements of the CW A

. Under 40 C.F .R. § 122.48(b), permits must specify “[ r] e quired monitoring including ty pe, intervals, a

nd frequency sufficient to y ield data which are representative o f the monitored a c tivity including
, when a p propriate,

c o n t i nu ous monitoring [ .] ” A permit must “assure compliance with [ the] permit limitations” by including r equirements toF O O D & W A T E R W A T C H V

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monitor the “mass (or other measurement specified in the permit) for e a ch pollutant limited in the permit; the volume of effluent discharg ed f

r om each outfall; other measurements

as appropriate.” 40 C.F .R. § 122.44( i ) ( 1 ) ( i)–(iii); see also U.S. EPA, NPD ES Permit W riters’ Manual at 8-2 (Sept. 2010), https://www.epa.g ov/sites/default/files/2015-09/doc uments/pwm_2010.pdf (“Monitoring is p erformed to determine compliance with effluent limitations established in NPDES permits, establish a b a s i s for enforcement a ctions,

assess treatment efficiency
, characteriz e effluents a nd characteriz e receiving

water.”).

This statutory and reg ulatory f ramework g ives discretion
to the EPA in crafting appropriate monitorin g requirements for each NPDES permit. H ow e v e r, the EPA’s discretion is
not unlimited. W hile 40 C.F .R. § 122.44(i) contemplates that the EPA has discret i o n to decide which monitoring requirements to include in an NPDES permit, 40 C.F .R. § 122.48(b) specifies that a p ermit must c o n t ai n monitoring provisions “sufficient to y ield [ representative] data.” See N L R B v. Brown
, 380 U .S. 278, 291 ( 1965) (“Reviewi n g courts are not oblig ed to stand aside and rubberstamp their affirmance of administrative decision s t h at they deem inconsistent with a statutory mandate o r that frustrate the
cong ressional p olicy underly ing a statute.”); Buffalo Crushed Ston e, Inc. v. Surface Transp. B d

. , 194 F .3d 125, 128–29 (D.C. Cir. 1999) (“[ D] e ference is not w ithout limit. W e will reject an a g ency ’s interpretation if an alternative r eading is compelled by the reg ulation’s plain lang uag e

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

Our c ase law confirms that NPDES p ermits must c ontain monitoring provisions sufficient to e n sure compliance with the terms of a permit. F or ex ample, in NRDC v

. County ofF O O D & W A T E R W A T C H V

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20

Los Angeles
, 725 F .3 d 1 1 9 4
, 1207 (9th Cir. 2013), we h eld that an NPDE S p e rmit is “ unlawful if a p ermittee is not required to effectively monitor its permit compliance.” W e

c o ncluded that the CW A “ requires every NPDES permi t t e e to monitor its discharg es into the n avig able waters of the United States in a manner sufficient to d etermine wh e t h er it is in compliance w i t h the r elevant NPDES permit.” Id.
at 1207 (emphasis in orig inal) (citing 33 U.S.C. § 1342(a)(2); 40 C.F .R. § 122.4 4 ( 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 i t m o n i tored compliance w ith the p ermit’s prohibition on the discharg e o f free oil).

Similarly
, in NRDC v

. U.S. EPA
, 808 F .3d 556, 583–84 (2d Cir. 2015), the Second Circuit rejected an NPDES p ermit because it lacked monitoring provisions. The EPA had issued

a g eneral p e rmit for the discharg e of b a l l a s t w aters from vessels. Id. a t 583. The permit r e q uired vessels to report the

ex p ected dates, times, locations, volumes, and salinities o f its discharg es. Id. B ut the r e q uired re ports provided little information on the quality of the ballast water. Id. B ecause the reports did not reveal whe t h er a v essel was actually in compliance with the effluent limitations, the p e rmit v iolated the statutory command that NPDES permits i nclude monitoring sufficient to ensure compliance with applicable effluent limitations. Id.

I ssuance of an NPDES permit is thus arbitrary
, capricious, and contrary to law if the permit fail s to include monitoring provisions that ensure compliance with the permit’s effluent limitations. As we have previ o u sly recog niz ed, “[ t] he NP DES prog ram f

undamentally relies on self-monitoring

. ” S i e r ra Club v. Union Oil Co. of Cal.
, 813 F .2d 1480, 1 4 9 1F O O D & W A T E R W A T C H V

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(9th Ci r. 1987), vacated and remanded on other grounds
, 485 U.S. 931 (1988), and reinsta t e d and amended by 853 F .2d 6 6 7 (9th Cir. 1988). Effective self-m o nitoring reveals permit violations, thereby promoting enforcement o f
t h e CW A. See id. at 1492; see also County of Los A ng e l e s , 725 F .3d at 1208 (“The [ Act] is v iewed by m a n y as the easiest of the federal environmental statutes to enforce. This is bec a u s e persons reg ulated under the act normally must repor t their own compliance a nd noncompliance to the
reg ulating ag ency .” (quotation marks a n d citation omitted)).

2. Monitoring Under the I daho Permit

The EPA d oes not quarrel with the foreg oing

. I t concedes that a permit must c ontain sufficient monitoring requirements
to ensure that a CAF O complies with the effluent limitations in its permit. However, the E PA arg ues that the I daho Permit contains sufficient monitoring requirements t o ensure compliance, and that we must defer to its ex pertise.

As described abov e , t h e I daho Permit requires CAF O operators to implement various m easures to prevent discharg es f

rom the production and l a n d -application areas. Petitioners arg ue the Permit does not require monitoring that would e nsure detection of u npermitted discharg es. We ag r ee with Petitioners.

a. Production Areas

The Permit has sufficient monitoring requiremen t s for above-g r ound discharg es from p roduction areas. As noted above, CAF O s are required to perform daily inspecti o ns o f
water lines, and w eekly inspections of storm water diversion devices, runoff diversion st r uctures, devices channelingF O O D & W A T E R W A T C H V

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22

contami nated storm w ater, and w aste storag e containers. These m a n dated inspections are, in effect, monitoring requirements. W e d efer to the EPA’s e x pertise and hold that these provisions are sufficient to ensure compliance with the Permit’s z e ro-discharg e ef f luent limitation from production

areas. F or ex ample, the visual inspection o f a waste container’s depth marker e n s u res that containers maintain
enoug h space to handle any ex c ess w ater, thereby preventing runoff in all but the ex treme circums t a n c e o f a 25-y ear, 24- hour rainfall event. See NRDC
, 863 F .2d at 1 433–34 (visual inspections that identify whether effluent limitation is met a re reasonable).

However, the Permit has no monitoring provisions for underg round discharg es from produc t i on areas. The record before the EPA showed that lea k y containment structures— especially lag oons—are sources o f g roundwater po l l u t i o n a nd that “g roundwater flow is the primary contributor of n i trate to surface water from ag riculture.” See Cow P a lace, LLC
, 80 F

. Supp. 3d at 1223. Despite this, the I d a h o P e rmit has no monitoring requirement for u n derg round discharg es. T h e failure o f the Permit to require s u c h monitoring is striking
, g iven the EPA’s conclusion in the 2003 Rule that requirements in local p ermits rather than nationally u niform requirements are the best means to a d d r ess underg r ound discharg es. I n reject i n g a p roposal that monitoring o f underg round discharg es b e included in the nationwide 2003 Rule, the EPA wrote:

The p roposed r

ul e would have imposed explicit na tional requirements for c ertain CAFOs to add

r ess possible discharges to surface water via ground waters that h a ve a direct hydrologic c onnection to surfaceF O O D & W A T E R W A T C H V

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waters

. These operations would have been required to sample g roundwaters. . . .

I n today ’ s effluent limitation g uidelines, EPA is rejecting e stablishing requirements related to discharg es to sur face water that

occur via ground water with a direct hy drolog ic connection.

Pollutan t discharg es from CAF Os to

s u r f a ce water via a g roundwater pathway a re hig hly dep e n dent on site-specific variables, such as topog raph y , climate, distance to

su r f a ce water, and g eolog ic factors such a s depth o f g roundwater, soil porosity a nd permeability
, and subsurface s t r u cture. The factors affecting w hether s uch discharg es a re occurring at CAF Os are so variable from site
to site that a national tec h nolog y -based standard is inappropriate.

2003 Rule at 7,216 (emphasis added); see also W aterkeeper
, 399 F

. 3d at 515 (“Studies do show tha t v a r i ability in topog raphy
, climate, distance to surface water, and g eolog ic factors influence whethe r a n d how pollutant discharg es a t a particular site enter surface water via g roundwater.”).

T he CW A r equires that the EPA ensure that e ve r y NPDES permittee “monitor its discharg es

. . . in a manner sufficient to determine whether it is in compliance w i th the relevant NPDES perm i t

. ” County of Los Angeles
, 725 F .3d

a t 1207. W ith one e x ception not r elevant here, the I d a h o Permit does not allow a n y d i s c h arg es from the production

area. W ithout a requirement t h a t CAF Os monitor wasteF O O D & W A T E R W A T C H V

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24

containment structures for underg roun d discharg e s, there is

no way to ensure that production are as comply w ith the Permit’s z ero-discharg e requirement. See W a t e rkeeper
, 399 F .3d a t 499 (failure of permit to include any mechanism for e v aluating c ompliance with e f fluent limitation was arbitrary and capricious).

b. L and-Application Areas

As noted above, CAF O reg ulations allow discharg es from CAF O land-appli c ation areas during w et weather, provided the CAF O has complied with its NMP. See 40 C.F .R. § 122.23(e) (“[ W ] h ere the manure, litter or pro c e s s wastewater has been applied in accordance with site specific nutrient manag ement practices

. . . a precipitation-re l a t ed discharg e of manure, litter or process wastewater fr o m land

areas under the control of a CAF O is an a gricultural
stormwater d ischarg e .”). However, the I daho Permit flatly prohibits discharg es from land-application areas d uring dry weather:

There shall be no dr y weather discharg e o f
manure, litter, o r process w astewater to a water of the United States f rom a CAF O as a

r e s u lt of the application o f manure, litter o r process w astewater to la n d a reas under the control of the CAF O. Th is prohibition includes discharg es t o w aters of the United States throug h tile drains, d itches or other
convey ances, and irrig a tion return.

The Permit has no monitoring provisions for dry weather di s c harg es f

rom land-application areas, even thoug h the record before the EPA showed that such discharg es can occurF O O D & W A T E R W A T C H V

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during irrig ation o f fertiliz ed CAF O fiel d s

. The Permit

assumes that because the NMP req u i r es CAF Os to a pply
manure, litter, and process wastewater at the ag ronomic rates established by the NMP, i r r i g ation-produced runoff o f pol l u t ants will never occur. There is little in the record to support that assumption. Without a requirement to m o n itor runoff from irrig ated CAF O fields, there is no way to ensure that a CAF O is comply ing with the Permit’s dry weather nodischarg e requirement for land-applic a tion areas. See Cnty.

o f L

. A.
, 725 F .3d at 1207 (holding that an NPDES per m i t must include compliance monitoring measures).

Conclusion

The I daho Permit fo r

b i d s underg r ound d ischarg es from production areas and dry w ea t h er discharg es from landa pplication areas. However, the Permit contains n o monitoring requirements for either kind of d i s c h arg e

. B ecause the Permit does not require mo n i toring that would

ensure c ompliance with its effluent li mitations, the E PA’s i s s u ance of the Permit w as arbitrary
, capricious, an d a violation of law. W e g rant the petition and vacate the Permit.

Petition G R

ANTED and Permit VACATED.