NATIONAL ASSOCIATION OF HOME BUILDERS et al. v. DEFENDERS OF WILDLIFE et al.

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NATIONAL ASSOCIATION OF HOME BUILDERS
et al. v. DEFENDERS OF WILDLIFE et al.
certiorari to the united states court of appeals for
the ninth circuit
No. 06–340. Argued April 17, 2007—Decided June 25, 2007*
Under the Clean Water Act (CWA), petitioner Environmental Protection
Agency (EPA) initially administers each State’s National Pollution Dis
charge Elimination System (NPDES) permitting program, but CWA
§ 402(b) provides that the EPA “shall approve” transfer of permitting
authority to a State upon application and a showing that the State has
met nine specified criteria. Section 7(a)(2) of the Endangered Species
Act of 1973 (ESA) requires federal agencies to consult with agencies
designated by the Secretaries of Commerce and the Interior to “insure”
that a proposed agency action is unlikely to jeopardize an endangered
or threatened species. The Fish and Wildlife Service (FWS) and the
National Marine Fisheries Service (NMFS) administer the ESA. Once
a consultation process is complete, a written biological opinion is issued,
which may suggest alternative actions to protect a jeopardized species
or its critical habitat. When Arizona officials sought EPA authorization
to administer the State’s NPDES program, the EPA initiated consulta
tion with the FWS to determine whether the transfer would adversely
affect any listed species. The FWS regional office wanted potential
impacts taken into account, but the EPA disagreed, finding that
§ 402(b)’s mandatory nature stripped it of authority to disapprove a
transfer based on any other considerations. The dispute was referred
to the agencies’ national offices for resolution. The FWS’ biological
opinion concluded that the requested transfer would not jeopardize
listed species. The EPA concluded that Arizona had met each of
§ 402(b)’s nine criteria and approved the transfer, noting that the biologi
cal opinion had concluded the consultation “required” by ESA § 7(a)(2).
Respondents sought review in the Ninth Circuit, petitioner National
Association of Home Builders intervened, and part of respondent De
fenders of Wildlife’s separate action was consolidated with the suit.
The court held that the EPA’s transfer approval was arbitrary and capri
cious because the EPA had relied on contradictory positions regarding
its § 7(a)(2) responsibilities during the administrative process. Rather
*Together with No. 06–549, Environmental Protection Agency v. De
fenders of Wildlife et al., also on certiorari to the same court.

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than remanding the case for the EPA to explain its decision, however,
the court reviewed the EPA’s substantive construction of the statutes.
It did not dispute that Arizona had met CWA § 402(b)’s nine criteria,
but nevertheless concluded that ESA § 7(a)(2) required the EPA to de
termine whether its transfer decision would jeopardize listed species, in
effect adding a tenth criterion. The court dismissed the argument that
the EPA’s approval was not subject to § 7(a)(2) because it was not a
“discretionary action” under 50 CFR § 402.03, § 7(a)(2)’s interpretative
regulation. The court thus vacated the EPA’s transfer decision.
Held:
1. The Ninth Circuit’s determination that the EPA’s action was arbi
trary and capricious is not fairly supported by the record. This Court
will not vacate an agency’s decision under the arbitrary and capricious
standard unless the agency “relied on factors which Congress had 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 ascribed to a difference in view or the product of agency expertise.”
Motor Vehicle Mfrs. Assn. of United States, Inc. v. State Farm Mut.
Automobile Ins. Co., 463 U. S. 29, 43. Here, the Ninth Circuit con
cluded that the EPA’s decision was internally inconsistent in its state
ments during the review process. Federal courts ordinarily are em
powered to review only an agency’s final action, and the fact that a local
agency representative’s preliminary determination is later overruled at
a higher agency level does not render the decisionmaking process arbi
trary and capricious. The EPA’s final approval notice stating that
§ 7(a)(2)’s required consultation process had been concluded may be in
consistent with its previously expressed position—and position in this
litigation—that § 7(a)(2)’s consultation requirement is not triggered by
a § 402 transfer application, but that is not the type of error requiring a
remand. By the time the statement was issued, the EPA and the FWS
had already consulted, and the question whether that consultation had
been required was not germane to the final agency decision. Thus, this
Court need not further delay the permitting authority transfer by re
manding to the EPA for clarification. Respondents suggest that the
EPA nullified their right to participate in the application proceedings
by altering its legal position during the pendency of the transfer deci
sion and its associated litigation, but they do not suggest that they were
deprived of their right to comment during the comment period made
available under the EPA’s regulations. Pp. 657–661.
2. Because § 7(a)(2)’s no-jeopardy duty covers only discretionary
agency actions, it does not attach to actions (like the NPDES permitting

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transfer authorization) that an agency is required by statute to undertake
once certain specified triggering events have occurred. Pp. 661–672.
(a) At first glance the legislative commands here are irreconcilable.
Section 402(b)’s “shall approve” language is mandatory and its list exclu
sive; if the nine specified criteria are satisfied, the EPA does not have
the discretion to deny a transfer application. Section 7(a)(2)’s similarly
imperative language would literally add a tenth criterion to § 402(b).
Pp. 661–662.
(b) While a later enacted statute (such as the ESA) can sometimes
operate to amend or even repeal an earlier statutory provision (such as
the CWA), “repeals by implication are not favored” and will not be pre
sumed unless the legislature’s intention “to repeal [is] clear and mani
fest.” Watt v. Alaska, 451 U. S. 259, 267. Statutory repeal will not be
inferred “unless the later statute ‘ “expressly contradict[s] the original
act” ’ or such a construction ‘ “is absolutely necessary [to give the later
statute’s words] any meaning at all.” ’ ” Traynor v. Turnage, 485 U. S.
535, 548. Otherwise, “a statute dealing with a narrow, precise, and spe
cific subject is not submerged by a later enacted statute covering a more
generalized spectrum.” Radzanower v. Touche Ross & Co., 426 U. S.
148, 153. The Ninth Circuit’s reading of § 7(a)(2) would effectively re
peal § 402(b)’s mandate that the EPA “shall” issue a permit whenever
all nine exclusive statutory prerequisites are met. Section 402(b) does
not just set minimum requirements; it affirmatively mandates a trans
fer’s approval, thus operating as a ceiling as well as a floor. By adding
an additional criterion, the Ninth Circuit raises that floor and alters
the statute’s command. Read broadly, the Ninth Circuit’s construction
would also partially override every federal statute mandating agency
action by subjecting such action to the further condition that it not jeop
ardize listed species. Pp. 662–664.
(c) Title 50 CFR § 402.03, promulgated by the NMFS and the FWS
and applying § 7(a)(2) “to all actions in which there is discretionary
Federal involvement or control” (emphasis added), harmonizes the CWA
and the ESA by giving effect to the ESA’s no-jeopardy mandate when
ever an agency has discretion to do so, but not when the agency is for
bidden from considering such extrastatutory factors. The Court owes
“some degree of deference to the Secretary’s reasonable interpretation”
of the ESA, Babbitt v. Sweet Home Chapter, Communities for Great
Ore., 515 U. S. 687, 703. Deference is not due if Congress has made its
intent “clear” in the statutory text, Chevron U. S. A. Inc. v. Natural
Resources Defense Council, Inc., 467 U. S. 837, 842, but “if the statute
is silent or ambiguous . . . the question . . . is whether the agency’s
answer is based on a permissible construction of the statute,” id., at 843.
Because the “meaning—or ambiguity—of certain words or phrases may

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only become evident . . . in context,” FDA v. Brown & Williamson
Tobacco Corp., 529 U. S. 120, 132, § 7(a)(2) must be read against the stat
utory backdrop of the many mandatory agency directives whose opera
tion it would implicitly abrogate or repeal were it construed as broadly
as the Ninth Circuit did below. Such a reading leaves a fundamental
ambiguity. An agency cannot simultaneously obey the differing man
dates of ESA § 7(a)(2) and CWA § 402(b), and consequently the statutory
language—read in light of the canon against implied repeals—does not
itself provide clear guidance as to which command must give way.
Thus, it is appropriate to look to the implementing agency’s expert in
terpretation, which harmonizes the statutes by applying § 7(a)(2) to
guide agencies’ existing discretionary authority, but not reading it to
override express statutory mandates. This interpretation is reasonable
in light of the statute’s text and the overall statutory scheme and is
therefore entitled to Chevron deference. The regulation’s focus on “dis
cretionary” actions accords with the commonsense conclusion that, when
an agency is required to do something by statute, it simply lacks the
power to “insure” that such action will not jeopardize listed species.
The basic principle of Department of Transportation v. Public Citizen,
541 U. S. 752—that an agency cannot be considered the legal “cause” of
an action that it has no statutory discretion not to take, id., at 770—
supports the reasonableness of the FWS’ interpretation. Pp. 664–669.
(d) Respondents’ contrary position is not supported by TVA v. Hill,
437 U. S. 153, which had no occasion to answer the question presented
in these cases. Pp. 669–671.
(e) Also unavailing is the argument that the EPA’s decision to
transfer NPDES permitting authority to Arizona represented a “discre
tionary” agency action. While the EPA may exercise some judgment
in determining whether a State has shown that it can carry out § 402(b)’s
enumerated criteria, the statute clearly does not grant it the discretion
to add another entirely separate prerequisite to that list. Nothing in
§ 402(b) authorizes the EPA to consider the protection of listed species
as an end in itself when evaluating a transfer application. And to the
extent that some of § 402(b)’s criteria may result in environmental bene
fits to marine species, Arizona has satisfied each of those criteria. Re
spondents’ argument has also been disclaimed by the FWS and the
NMFS, the agencies primarily charged with administering § 7(a)(2) and
the drafters of the regulations implementing that section. Pp. 671–672.
420 F. 3d 946, reversed and remanded.
Alito, J., delivered the opinion of the Court, in which Roberts, C. J.,
and Scalia, Kennedy, and Thomas, JJ., joined. Stevens, J., filed a dis

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senting opinion, in which Souter, Ginsburg, and Breyer, JJ., joined,
post, p. 673. Breyer, J., filed a dissenting opinion, post, p. 698.
Deputy Solicitor General Kneedler argued the cause for
petitioners in both cases. With him on the briefs for peti
tioner Environmental Protection Agency were Solicitor
General Clement, Acting Assistant Attorney General Mc-
Keown, Malcolm L. Stewart, Andrew C. Mergen, and David
C. Shilton. Norman D. James, Duane J. Desider io,
Thomas J. Ward, and Russell S. Frye filed briefs for peti
tioners National Association of Home Builders et al. in
No. 06–340. Terry Goddard, Attorney General of Arizona,
Mary O’Grady, Solicitor General, Paula Bickett, Chief Coun
sel, and James T. Skardon, Assistant Attorney General, filed
briefs for the State of Arizona as respondent under this
Court’s Rule 12.6, in support of petitioners.
Eric R. Glitzenstein argued the cause for respondents in
both cases. With him on the brief were Katherine A. Meyer
and Michael P. Senatore.†
†Briefs of amici curiae urging reversal in both cases were filed for the
State of Nebraska et al. by Jon C. Bruning, Attorney General of Ne
braska, David D. Cookson, Assistant Attorney General, and Donald G.
Blankenau and Thomas R. Wilmoth, Special Assistant Attorneys Gen
eral, by Roberto J. Sa´ nchez-Ramos, Secretary of Justice of Puerto Rico,
and by the Attorneys General and other officials for their respective States
as follows: Troy King of Alabama, Talis J. Colberg of Alaska, John W.
Suthers of Colorado, Lawrence Wasden of Idaho, Jeremiah W. (Jay) Nixon
of Missouri, Catherine Cortez Masto of Nevada, Gary K. King of New
Mexico, and Stephen R. Farris and Frances C. Bassett, Assistant Attor
neys General of New Mexico, Wayne Stenehjem of North Dakota, Robert
E. Cooper, Jr., of Tennessee, Mark L. Shurtleff of Utah, and Patrick J.
Crank of Wyoming; for the American Farm Bureau Federation by Ellen
Steen and Thomas R. Lundquist; for the American Road and Transporta
tion Builders Association et al. by Lawrence R. Liebesman and Nick Gold
stein; for the Arizona Power Authority et al. by Virginia S. Albrecht,
Karma B. Brown, and Kathy Robb; for the Association of California Water
Agencies et al. by Roderick E. Walston, Karen L. Tachiki, John C. Clair
day, Linus Masouredis, Daniel O’Hanlon, Christopher Onstott, Daniel S.
Hentschke, Peter D. Nichols, Robert V. Trout, and Peggy E. Montano; for
CropLife America by Douglas T. Nelson, Steven P. Quarles, and J. Mi

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Opinion of the Court
Justice Alito delivered the opinion of the Court.
These cases concern the interplay between two federal en
vironmental statutes. Section 402(b) of the Clean Water
Act requires that the Environmental Protection Agency
transfer certain permitting powers to state authorities upon
an application and a showing that nine specified criteria have
been met. Section 7(a)(2) of the Endangered Species Act of
1973 provides that a federal agency must consult with agen
cies designated by the Secretaries of Commerce and the In
terior in order to “insure that any action authorized, funded,
or carried out by such agency . . . is not likely to jeopardize
the continued existence of any endangered species or threat
ened species.” The question presented is whether § 7(a)(2)
effectively operates as a tenth criterion on which the trans
fer of permitting power under the first statute must be con
ditioned. We conclude that it does not. The transfer of
permitting authority to state authorities—who will exercise
that authority under continuing federal oversight to ensure
compliance with relevant mandates of the Endangered Spe
chael Klise; for the Federal Water Quality Coalition by Daniel P. Albers;
for High Production Homebuilders by Carter G. Phillips, Stephen M.
Nickelsburg, and Eric A. Shumsky; for the National Hydropower Associa
tion et al. by Sam Kalen and Michael A. Swiger; for the Washington Legal
Foundation et al. by Daniel J. Popeo and Richard A. Samp; and for the
Western Urban Water Coalition by Benjamin S. Sharp and Guy R.
Martin.
M. Reed Hopper filed a brief for the Pacific Legal Foundation as amicus
curiae urging reversal in No. 06–340.
Roger J. Marzulla and Nancie G. Marzulla filed a brief for the Kern
County Water Agency et al. as amici curiae urging reversal in No. 06–549.
Briefs of amici curiae urging affirmance in both cases were filed for the
American Bird Conservancy et al. by Michael J. Bean; and for Jared M.
Diamond et al. by Daniel J. Rohlf.
Briefs of amici curiae were filed in both cases for the American Fish
eries Society et al. by Jan E. Hasselman, Patti A. Goldman, John F.
Kostyack, and Mary Randolph Sargent; for the Mountain States Legal
Foundation by William Perry Pendley; and for the National Association
of Clean Water Agencies by William A. Anderson II, Sean M. Sullivan,
D. Cameron Prell, and Alexandra D. Dunn.

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cies Act and other federal environmental protection stat
utes—was proper. We therefore reverse the judgment
of the United States Court of Appeals for the Ninth Circuit.
I
A
1
The Clean Water Act (CWA), 86 Stat. 816, as amended, 33
U. S. C. § 1251 et seq., established a National Pollution Dis
charge Elimination System (NPDES) that is designed to pre
vent harmful discharges into the Nation’s waters. The En
vironmental Protection Agency (EPA or Agency) initially
administers the NPDES permitting system for each State,
but a State may apply for a transfer of permitting authority
to state officials. See 33 U. S. C. § 1342; see also § 1251(b)
(“It is the policy of Congress that the Stat[e] . . . implement
the permit progra[m] under sectio[n] 1342 . . . of this title”).
If authority is transferred, then state officials—not the fed
eral EPA—have the primary responsibility for reviewing
and approving NPDES discharge permits, albeit with contin
uing EPA oversight.1
Under § 402(b) of the CWA, “the Governor of each State
desiring to administer its own permit program for discharges
into navigable waters within its jurisdiction may submit to
[the EPA] a full and complete description of the program it
proposes to establish and administer under State law or
under an interstate compact,” as well as a certification “that
the laws of such State . . . provide adequate authority to
carry out the described program.” 33 U. S. C. § 1342(b).
The same section provides that the EPA “shall approve each
submitted program” for transfer of permitting authority to
1 The State must advise the EPA of each permit it proposes to issue,
and the EPA may object to any permit. 33 U. S. C. §§ 1342(d)(1), (2); see
also 40 CFR § 123.44(c) (2006). If the State cannot address the EPA’s
concerns, authority over the permit reverts to the EPA. 33 U. S. C.
§ 1342(d)(4).

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a State “unless [it] determines that adequate authority does
not exist” to ensure that nine specified criteria are satisfied.
Ibid. These criteria all relate to whether the state agency
that will be responsible for permitting has the requisite au
thority under state law to administer the NPDES program.2
If the criteria are met, the transfer must be approved.
2
The Endangered Species Act of 1973 (ESA), 87 Stat. 884,
as amended, 16 U. S. C. § 1531 et seq., is intended to protect
and conserve endangered and threatened species and their
habitats. Section 4 of the ESA directs the Secretaries of
Commerce and the Interior to list threatened and endan
gered species and to designate their critical habitats.
§ 1533. The Fish and Wildlife Service (FWS) administers
the ESA with respect to species under the jurisdiction of the
Secretary of the Interior, while the National Marine Fisher
ies Service (NMFS) administers the ESA with respect to
species under the jurisdiction of the Secretary of Commerce.
See 50 CFR §§ 17.11, 222.101(a), 223.102, 402.01(b) (2006).
2 The State must demonstrate that it has the ability: (1) to issue fixed
term permits that apply and ensure compliance with the CWA’s substan
tive requirements and which are revocable for cause; (2) to inspect, moni
tor, and enter facilities and to require reports to the extent required by
the CWA; (3) to provide for public notice and public hearings; (4) to ensure
that the EPA receives notice of each permit application; (5) to ensure that
any other State whose waters may be affected by the issuance of a permit
may submit written recommendations and that written reasons be pro
vided if such recommendations are not accepted; (6) to ensure that no
permit is issued if the Army Corps of Engineers concludes that it would
substantially impair the anchoring and navigation of navigable waters;
(7) to abate violations of permits or the permit program, including through
civil and criminal penalties; (8) to ensure that any permit for a discharge
from a publicly owned treatment works includes conditions requiring
the identification of the type and volume of certain pollutants; and
(9) to ensure that any industrial user of any publicly owned treatment
works will comply with certain of the CWA’s substantive provisions.
§§ 1342(b)(1)–(9).

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Section 7 of the ESA prescribes the steps that federal
agencies must take to ensure that their actions do not jeopar
dize endangered wildlife and flora. Section 7(a)(2) provides
that “[e]ach Federal agency shall, in consultation with and
with the assistance of the Secretary [of Commerce or the
Interior], insure that any action authorized, funded, or car
ried out by such agency (hereinafter in this section referred
to as an ‘agency action’) is not likely to jeopardize the contin
ued existence of any endangered species or threatened spe
cies.” 16 U. S. C. § 1536(a)(2).
Once the consultation process contemplated by § 7(a)(2)
has been completed, the Secretary is required to give the
agency a written biological opinion “setting forth the Secre
tary’s opinion, and a summary of the information on which
the opinion is based, detailing how the agency action affects
the species or its critical habitat.” § 1536(b)(3)(A); see also
50 CFR § 402.14(h). If the Secretary concludes that the
agency action would place the listed species in jeopardy or
adversely modify its critical habitat, “the Secretary shall
suggest those reasonable and prudent alternatives which he
believes would not violate [§ 7(a)(2)] and can be taken by the
Federal agency . . . in implementing the agency action.” 16
U. S. C. § 1536(b)(3)(A); see also 50 CFR § 402.14(h)(3). Reg
ulations promulgated jointly by the Secretaries of Commerce
and the Interior provide that, in order to qualify as a “rea
sonable and prudent alternative,” an alternative course of
action must be able to be implemented in a way “consistent
with the scope of the Federal agency’s legal authority and
jurisdiction.” § 402.02. Following the issuance of a “jeop
ardy” opinion, the agency must either terminate the action,
implement the proposed alternative, or seek an exemption
from the Cabinet-level Endangered Species Committee pur
suant to 16 U. S. C. § 1536(e). The regulations also provide
that “Section 7 and the requirements of this part apply to all
actions in which there is discretionary Federal involvement
or control.” 50 CFR § 402.03.

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B
1
In February 2002, Arizona officials applied for EPA au
thorization to administer that State’s NPDES program.3
The EPA initiated consultation with the FWS to determine
whether the transfer of permitting authority would ad
versely affect any listed species.
The FWS regional office concluded that the transfer of au
thority would not cause any direct impact on water quality
that would adversely affect listed species. App. to Pet. for
Cert. in No. 06–340, p. 564. However, the FWS office was
concerned that the transfer could result in the issuance of
more discharge permits, which would lead to more develop
ment, which in turn could have an indirect adverse effect
on the habitat of certain upland species, such as the cactus
ferruginous pygmy-owl and the Pima pineapple cactus.
Specifically, the FWS feared that, because § 7(a)(2)’s consul
tation requirement does not apply to permitting decisions by
state authorities,4 the transfer of authority would empower
Arizona officials to issue individual permits without consider
ing and mitigating their indirect impact on these upland spe
cies. Id., at 565–566. The FWS regional office therefore
urged that, in considering the proposed transfer of permit
ting authority, those involved in the consultation process
should take these potential indirect impacts into account.
The EPA disagreed, maintaining that “its approval action,
which is an administrative transfer of authority, [would not
be] the cause of future non-discharge-related impacts on en
dangered species from projects requiring State NPDES per
mits.” Id., at 564. As a factual matter, the EPA believed
3 At the time when Arizona applied, the EPA had already transferred
permitting authority to local authorities in 44 other States and several
United States Territories.
4 By its terms, § 7(a)(2)’s consultation requirement applies only to “ac
tion[s] authorized, funded, or carried out” by “Federal agenc[ies].”

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that the link between the transfer of permitting authority
and the potential harm that could result from increased de
velopment was too attenuated. Ibid. And as a legal mat
ter, the EPA concluded that the mandatory nature of CWA
§ 402(b)—which directs that the EPA “shall approve” a
transfer request if that section’s nine statutory criteria are
met—stripped it of authority to disapprove a transfer based
on any other considerations. Id., at 564–565.
Pursuant to procedures set forth in a memorandum of un
derstanding between the agencies, the dispute was referred
to the agencies’ national offices for resolution. In December
2002, the FWS issued its biological opinion, which concluded
that the requested transfer would not cause jeopardy to
listed species. The opinion reasoned that “the loss of sec
tion 7-related conservation benefits . . . is not an indirect
effect of the authorization action,” id., at 117, because
“loss of any conservation benefit is not caused by EPA’s
decision to approve the State of Arizona’s program.
Rather, the absence of the section 7 process that exists
with respect to Federal NPDES permits reflects Con
gress’ decision to grant States the right to administer
these programs under state law provided the State’s
program meets the requirements of [section] 402(b) of
the Clean Water Act.” Id., at 114.
In addition, the FWS opined that the EPA’s continuing
oversight of Arizona’s permitting program, along with other
statutory protections, would adequately protect listed spe
cies and their habitats following the transfer. Id., at
101–107.
The EPA concluded that Arizona had met each of the nine
statutory criteria listed in § 402(b) and approved the transfer
of permitting authority. In the notice announcing the ap
proval of the transfer, the EPA noted that the issuance of
the FWS’ biological opinion had “conclude[d] the consulta
tion process required by ESA section 7(a)(2) and reflects the

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[FWS’] agreement with EPA that the approval of the State
program meets the substantive requirements of the ESA.”
Id., at 73.
2
On April 2, 2003, respondents filed a petition in the United
States Court of Appeals for the Ninth Circuit seeking review
of the transfer pursuant to 33 U. S. C. § 1369(b)(1)(D), which
allows private parties to seek direct review of the EPA’s de
terminations regarding state permitting programs in the
federal courts of appeals. The court granted petitioner Na
tional Association of Home Builders leave to intervene as a
respondent in that case. Respondent Defenders of Wildlife
also filed a separate action in the United States District
Court for the District of Arizona, alleging, among other
things, that the biological opinion issued by the FWS in sup
port of the proposed transfer did not comply with the ESA’s
standards. The District Court severed that claim and trans
ferred it to the Court of Appeals for the Ninth Circuit, which
consolidated the case with the suit challenging the EPA
transfer. See 420 F. 3d 946 (2005).
A divided panel of the Ninth Circuit held that the EPA’s
approval of the transfer was arbitrary and capricious be
cause the EPA “relied during the administrative proceedings
on legally contradictory positions regarding its section 7 obli
gations.” Id., at 959. The court concluded that the EPA
“fail[ed] to understand its own authority under section 7(a)(2)
to act on behalf of listed species and their habitat,” id., at
977, because “the two propositions that underlie the EPA’s
action—that (1) it must, under the [ESA], consult concerning
transfers of CWA permitting authority, but (2) it is not per
mitted, as a matter of law, to take into account the impact
on listed species in making the transfer decision—cannot
both be true,” id., at 961. The court therefore concluded
that it was required to “remand to the agency for a plausible
explanation of its decision, based on a single, coherent inter
pretation of the statute.” Id., at 962.

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The panel majority, however, did not follow this course of
action. Rather, the panel went on to review the EPA’s sub
stantive construction of the statutes at issue and held that
the ESA granted the EPA both the power and the duty to
determine whether its transfer decision would jeopardize
threatened or endangered species. The panel did not dis
pute that Arizona had met the nine criteria set forth in
§ 402(b) of the CWA, but the panel nevertheless concluded
that § 7(a)(2) of the ESA provided an “affirmative grant of
authority to attend to [the] protection of listed species,” id.,
at 965, in effect adding a tenth criterion to those specified in
§ 402(b). The panel dismissed the argument that the EPA’s
approval of the transfer application was not subject to
§ 7(a)(2) because it was not a “discretionary action” within
the meaning of 50 CFR § 402.03 (interpreting § 7(a)(2) to
apply only to agency actions “in which there is discretionary
Federal involvement or control”). 420 F. 3d, at 967–969. It
viewed the FWS’ regulation as merely “coterminous” with
the express statutory language encompassing all agency ac
tions that are “ ‘authorized, funded, or carried out’ ” by the
agency. Id., at 969 (quoting 16 U. S. C. § 1536(a)(2)). On
these grounds, the court granted the petition and vacated
the EPA’s transfer decision.
In dissent, Judge Thompson explained that the transfer
decision was not a “discretionary action” under 50 CFR
§ 402.03 because “[t]he Clean Water Act, by its very terms,
permits the EPA to consider only the nine specified factors.
If a state’s proposed permitting program meets the enumer
ated requirements,” he reasoned, “the EPA administrator
‘shall approve’ the program. 33 U. S. C. § 1342(b). This
[c]ongressional directive does not permit the EPA to impose
additional conditions.” 420 F. 3d, at 980.
The Ninth Circuit denied rehearing and rehearing en banc.
450 F. 3d 394 (2006). Writing for the six judges who dis
sented from the denial of rehearing en banc, Judge Kozinski
disagreed with the panel’s conclusion that the EPA’s analysis

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was so internally inconsistent as to be arbitrary and capri
cious. He further noted that, if the panel was correct on
this point, the proper resolution would have been to remand
to the EPA for further explanation. Id., at 396–398. On
the statutory question, Judge Kozinski echoed Judge Thomp
son’s conclusion that once the nine criteria set forth in
§ 402(b) of the CWA are satisfied, a transfer is mandatory
and nondiscretionary. Id., at 397–399. He rejected the
panel majority’s broad construction of ESA § 7(a)(2), conclud
ing that “[i]f the ESA were as powerful as the majority con
tends, it would modify not only the EPA’s obligation under
the CWA, but every categorical mandate applicable to every
federal agency.” Id., at 399, n. 4.
The Ninth Circuit’s construction of § 7(a)(2) is at odds with
that of other Courts of Appeals. Compare 420 F. 3d 946
(case below) with Platte River Whooping Crane Critical
Habitat Maintenance Trust v. FERC, 962 F. 2d 27, 33–34
(CADC 1992), and American Forest & Paper Assn. v. EPA,
137 F. 3d 291, 298–299 (CA5 1998). We granted certiorari
to resolve this conflict, 549 U. S. 1105 (2007), and we now
reverse.
II
Before addressing this question of statutory interpreta
tion, however, we first consider whether the Court of Ap
peals erred in holding that the EPA’s transfer decision was
arbitrary and capricious because, in that court’s words, the
agencies involved in the decision “relied . . . on legally contra
dictory positions regarding [their] section 7 obligations.”
App. to Pet. for Cert. in No. 06–340, at 23.
As an initial matter, we note that if the EPA’s action was
arbitrary and capricious, as the Ninth Circuit held, the
proper course would have been to remand to the Agency for
clarification of its reasons. See Gonzales v. Thomas, 547
U. S. 183 (2006) (per curiam). Indeed, the court below ex
pressly recognized that this finding required it to “remand
to the Agency for a plausible explanation of its decision,

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based on a single, coherent interpretation of the statute.”
App. to Pet. for Cert. in No. 06–340, at 28. But the Ninth
Circuit did not take this course; instead, it jumped ahead to
resolve the merits of the dispute. In so doing, it erroneously
deprived the Agency of its usual administrative avenue for
explaining and reconciling the arguably contradictory ration
ales that sometimes appear in the course of lengthy and com
plex administrative decisions. We need not examine this
question further, however, because we conclude that the
Ninth Circuit’s determination that the EPA’s action was arbi
trary and capricious is not fairly supported by the record.
Review under the arbitrary and capricious standard is def
erential; we will not vacate an agency’s decision unless it
“has relied on factors which Congress had not intended
it to consider, entirely failed to consider an important
aspect of the problem, offered an explanation for its deci
sion that runs counter to the evidence before the agency,
or is so implausible that it could not be ascribed to a
difference in view or the product of agency expertise.”
Motor Vehicle Mfrs. Assn. of United States, Inc. v. State
Farm Mut. Automobile Ins. Co., 463 U. S. 29, 43 (1983).
“We will, however, ‘uphold a decision of less than ideal clarity
if the agency’s path may reasonably be discerned.’ ” Ibid.
(quoting Bowman Transp., Inc. v. Arkansas-Best Freight
System, Inc., 419 U. S. 281, 286 (1974)).
The Court of Appeals concluded that the EPA’s decision
was “internally inconsistent” because, in its view, the
Agency stated—both during preliminary review of Arizona’s
transfer application and in the Federal Register notice me
morializing its final action—“that section 7 requires consul
tation regarding the effect of a permitting transfer on listed
species.” App. to Pet. for Cert. in No. 06–340, at 23.
With regard to the various statements made by the in
volved agencies’ regional offices during the early stages of
consideration, the only “inconsistency” respondents can point

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to is the fact that the agencies changed their minds—some
thing that, as long as the proper procedures were followed,
they were fully entitled to do. The federal courts ordinarily
are empowered to review only an agency’s final action, see
5 U. S. C. § 704, and the fact that a preliminary determination
by a local agency representative is later overruled at a
higher level within the agency does not render the decision
making process arbitrary and capricious.
Respondents also point to the final Federal Register notice
memorializing the EPA’s approval of Arizona’s transfer ap
plication. This notice stated that the FWS’ issuance of its
biological opinion had “conclude[d] the consultation process
required by ESA section 7(a)(2).” App. to Pet. for Cert. in
No. 06–340, at 73. Respondents contend that this statement
is inconsistent with the EPA’s previously expressed posi
tion—and their position throughout this litigation—that
§ 7(a)(2)’s consultation requirement is not triggered by a
transfer application under § 402 of the CWA.
We are not persuaded that this statement constitutes the
type of error that requires a remand. By the time the Fed
eral Register statement was issued, the EPA had already
consulted with the FWS about the Arizona application, and
the question whether that consultation had been required, as
opposed to voluntarily undertaken by the Agency, was sim
ply not germane to the final agency transfer decision. The
Federal Register statement, in short, was dictum, and it had
no bearing on the final agency action that respondents chal
lenge. Mindful of Congress’ admonition that in reviewing
agency action, “due account shall be taken of the rule of prej
udicial error,” 5 U. S. C. § 706, we do not believe that this
stray statement, which could have had no effect on the un
derlying agency action being challenged, requires that we
further delay the transfer of permitting authority to Arizona
by remanding to the Agency for clarification. See also PDK
Labs. Inc. v. United States Drug Enforcement Admin., 362
F. 3d 786, 799 (CADC 2004) (“In administrative law, as in

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federal civil and criminal litigation, there is a harmless
error rule”).5
We further disagree with respondents’ suggestion that, by
allegedly altering its legal position while the Arizona trans
fer decision and its associated litigation was pending, the
“EPA is effectively nullifying respondents’ rights to partici
pate in administrative proceedings concerning Arizona’s ap
plication, and particularly respondents’ rights under EPA’s
own regulations to comment on NPDES transfer applica
tions.” Brief for Respondents 28 (citing 40 CFR § 123.61(b);
emphasis deleted). Consistent with EPA regulations, the
Agency made available “a comment period of not less than 45
days during which interested members of the public [could]
express their views on the State program.” § 123.61(a)(1).
Respondents do not suggest that they were deprived of their
right to comment during this period.6
5 We also note that the agencies involved have resolved any ambiguity
in their positions going forward. Following the issuance of the panel’s
opinion below, the EPA—in connection with the State of Alaska’s pending
application for transfer of NPDES permitting authority—requested con
firmation from the FWS and the NMFS of the EPA’s position that “the
no-jeopardy and consultation duties of ESA Section 7(a)(2) do not apply
to approval of a State’s application to administer the NPDES program,”
in the apparent hope that obtaining those agencies’ views “in advance of
processing Alaska’s application may avoid a repetition of ” the confusion
that occurred during the Arizona permitting process. App. to Pet. for
Cert. in No. 06–549, pp. 96a, 95a. In response, both the FWS and the
NMFS confirmed their understanding that “there is no need to conduct
Section 7 consultations on proposed actions to approve State NPDES pro
grams because such actions are not the cause of any impact on listed spe
cies and do not constitute discretionary federal agency actions to which
Section 7 applies.” Id., at 107a; see also id., at 116a (NMFS “concur[s]
with EPA’s conclusion that EPA is not required to engage in section 7
consultation on applications to approve State programs in situations under
Section 402(b) of the CWA”).
6 Nor is there any independent right to public comment with regard to
consultations conducted under § 7(a)(2)—a consultation process that we
conclude, in any case, was not required here. See 51 Fed. Reg. 19928
(1986) (“Nothing in section 7 authorizes or requires the Service to provide

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Respondents also contend that if the case were remanded
to the EPA, they would raise additional challenges—includ
ing, for example, a challenge to the EPA’s provision of fi
nancial assistance to Arizona for the administration of its
NPDES program. However, as explained below, any such
agency action is separate and independent of the agency’s
decision to authorize the transfer of permitting authority
pursuant to § 402(b). See n. 11, infra. We express no opin
ion as to the viability of a separate administrative or legal
challenge to such actions.
III
A
We turn now to the substantive statutory question raised
by the petitions, a question that requires us to mediate a
clash of seemingly categorical—and, at first glance, irrecon
cilable—legislative commands. Section 402(b) of the CWA
provides, without qualification, that the EPA “shall approve”
a transfer application unless it determines that the State
lacks adequate authority to perform the nine functions speci
fied in the section. 33 U. S. C. § 1342(b). By its terms, the
statutory language is mandatory and the list exclusive; if the
nine specified criteria are satisfied, the EPA does not have
the discretion to deny a transfer application. Cf. Lopez v.
Davis, 531 U. S. 230, 241 (2001) (noting Congress’ “use of a
mandatory ‘shall’ . . . to impose discretionless obligations”);
Lexecon Inc. v. Milberg Weiss Bershad Hynes & Lerach, 523
U. S. 26, 35 (1998) (“[T]he mandatory ‘shall’ . . . normally
creates an obligation impervious to judicial discretion”); As
sociation of Civil Technicians v. FLRA, 22 F. 3d 1150, 1153
(CADC 1994) (“The word ‘shall’ generally indicates a com
mand that admits of no discretion on the part of the person
instructed to carry out the directive”); Black’s Law Diction
ary 1375 (6th ed. 1990) (“As used in statutes . . . this word is
for public involvement (other than that of the applicant) in the ‘inter
agency’ consultation process”).

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generally imperative or mandatory”). Neither respondents
nor the Ninth Circuit has ever disputed that Arizona satis
fied each of these nine criteria. See 420 F. 3d, at 963, n. 11;
Brief for Respondents 19, n. 8.
The language of § 7(a)(2) of the ESA is similarly impera
tive: It provides that “[e]ach Federal agency shall, in consul
tation with and with the assistance of the Secretary, insure
that any action authorized, funded, or carried out by such
agency . . . is not likely to jeopardize” endangered or threat
ened species or their habitats. 16 U. S. C. § 1536(a)(2). This
mandate is to be carried out through consultation and may
require the agency to adopt an alternative course of action.
As the author of the panel opinion below recognized, apply
ing this language literally would “ad[d] one [additional] re
quirement to the list of considerations under the Clean Water
Act permitting transfer provision.” 450 F. 3d, at 404, n. 2
(Berzon, J., concurring in denial of rehearing en banc) (em
phasis in original). That is, it would effectively repeal the
mandatory and exclusive list of criteria set forth in § 402(b),
and replace it with a new, expanded list that includes
§ 7(a)(2)’s no-jeopardy requirement.
B
While a later enacted statute (such as the ESA) can some
times operate to amend or even repeal an earlier statutory
provision (such as the CWA), “repeals by implication are not
favored” and will not be presumed unless the “intention of
the legislature to repeal [is] clear and manifest.” Watt v.
Alaska, 451 U. S. 259, 267 (1981) (internal quotation marks
omitted). We will not infer a statutory repeal “unless the
later statute ‘ “expressly contradict[s] the original act” ’ or
unless such a construction ‘ “is absolutely necessary . . . in
order that [the] words [of the later statute] shall have any
meaning at all.” ’ ” Traynor v. Turnage, 485 U. S. 535, 548
(1988) (quoting Radzanower v. Touche Ross & Co., 426 U. S.

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148, 153 (1976), in turn quoting T. Sedgwick, The Interpreta
tion and Construction of Statutory and Constitutional Law
98 (2d ed. 1874)); see also Branch v. Smith, 538 U. S. 254, 273
(2003) (“An implied repeal will only be found where provi
sions in two statutes are in ‘irreconcilable conflict,’ or where
the latter Act covers the whole subject of the earlier one and
‘is clearly intended as a substitute’ ”); Posadas v. National
City Bank, 296 U. S. 497, 503 (1936) (“[T]he intention of the
legislature to repeal must be clear and manifest”). Outside
these limited circumstances, “a statute dealing with a nar
row, precise, and specific subject is not submerged by a later
enacted statute covering a more generalized spectrum.”
Radzanower, supra, at 153.
Here, reading § 7(a)(2) as the Court of Appeals did would
effectively repeal § 402(b)’s statutory mandate by engrafting
a tenth criterion onto the CWA.7 Section 402(b) of the CWA
commands that the EPA “shall” issue a permit whenever
all nine exclusive statutory prerequisites are met. Thus,
§ 402(b) does not just set forth minimum requirements for
the transfer of permitting authority; it affirmatively man
dates that the transfer “shall” be approved if the specified
criteria are met. The provision operates as a ceiling as well
as a floor. By adding an additional criterion, the Ninth Cir
7 Justice Stevens’ dissenting opinion (hereinafter dissent) attempts
to paper over this conflict by suggesting that the EPA and the agencies
designated by the Secretary of the Interior could reconcile the commands
of the CWA and the ESA by “generat[ing] an alternative course of action
whereby the transfer could still take place . . . but in such a way that
would honor the mandatory requirements of § 7(a)(2).” Post, at 687. For
example, it suggests that the EPA could condition transfers of permitting
authority on the State’s acceptance of additional continuing oversight by
the EPA (presumably beyond that oversight already contemplated by the
CWA’s statutory language). Post, at 688–690. But such a take-it-or
leave-it approach, no less than a straightforward rejection of a transfer
application, would impose conditions on an NPDES transfer beyond those
set forth in § 402(b), and thus alter the CWA’s statutory command.

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cuit’s construction of § 7(a)(2) raises that floor and alters
§ 402(b)’s statutory command.8
The Ninth Circuit’s reading of § 7(a)(2) would not only ab
rogate § 402(b)’s statutory mandate, but also result in the
implicit repeal of many additional otherwise categorical stat
utory commands. Section 7(a)(2) by its terms applies to
“any action authorized, funded, or carried out by” a federal
agency—covering, in effect, almost anything that an agency
might do. Reading the provision broadly would thus par
tially override every federal statute mandating agency ac
tion by subjecting such action to the further condition that
it pose no jeopardy to endangered species. See, e. g., Platte
River Whooping Crane Critical Habitat Maintenance Trust
v. FERC, 962 F. 2d, at 33–34 (considering whether § 7(a)(2)
overrides the Federal Power Act’s prohibition on amending
annual power licenses). While the language of § 7(a)(2) does
not explicitly repeal any provision of the CWA (or any other
statute), reading it for all that it might be worth runs four
square into our presumption against implied repeals.
C
1
The agencies charged with implementing the ESA have
attempted to resolve this tension through regulations imple
8 It does not matter whether this alteration is characterized as an
amendment or a partial repeal. Every amendment of a statute effects a
partial repeal to the extent that the new statutory command displaces
earlier, inconsistent commands, and we have repeatedly recognized that
implied amendments are no more favored than implied repeals. See, e. g.,
Regional Rail Reorganization Act Cases, 419 U. S. 102, 134 (1974) (“ ‘A
new statute will not be read as wholly or even partially amending a prior
one unless there exists a “positive repugnancy” between the provisions of
the new and those of the old that cannot be reconciled’ ” (quoting In re
Penn Central Transp. Co., 384 F. Supp. 895, 943 (Sp. Ct. R. R. R. A. 1974)));
United States v. Welden, 377 U. S. 95, 103, n. 12 (1964) (“Amendments by
implication . . . are not favored”); United States v. Madigan, 300 U. S. 500,
506 (1937) (“[T]he modification by implication of the settled construction
of an earlier and different section is not favored”).

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menting § 7(a)(2). The NMFS and the FWS, acting jointly
on behalf of the Secretaries of Commerce and the Interior
and following notice-and-comment rulemaking procedures,
have promulgated a regulation stating that “Section 7 and
the requirements of this part apply to all actions in which
there is discretionary Federal involvement or control.” 50
CFR § 402.03 (emphasis added). Pursuant to this regula
tion, § 7(a)(2) would not be read as impliedly repealing non
discretionary statutory mandates, even when they might re
sult in some agency action. Rather, the ESA’s requirements
would come into play only when an action results from the
exercise of agency discretion. This interpretation harmo
nizes the statutes by giving effect to the ESA’s no-jeopardy
mandate whenever an agency has discretion to do so, but not
when the agency is prohibited from considering such extra
statutory factors.
We have recognized that “[t]he latitude the ESA gives the
Secretary in enforcing the statute, together with the degree
of regulatory expertise necessary to its enforcement, estab
lishes that we owe some degree of deference to the Secre
tary’s reasonable interpretation” of the statutory scheme.
Babbitt v. Sweet Home Chapter, Communities for Great
Ore., 515 U. S. 687, 703 (1995). But such deference is appro
priate only where “Congress has not directly addressed the
precise question at issue” through the statutory text. Chev
ron U. S. A. Inc. v. Natural Resources Defense Council, Inc.,
467 U. S. 837, 843 (1984).
“If the intent of Congress is clear, that is the end of
the matter; for the court, as well as the agency, must
give effect to the unambiguously expressed intent of
Congress. . . . [However,] if the statute is silent or am
biguous with respect to the specific issue, the question
for the court is whether the agency’s answer is based
on a permissible construction of the statute.” Id., at
842–843.

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In making the threshold determination under Chevron,
“a reviewing court should not confine itself to examining
a particular statutory provision in isolation.” FDA v.
Brown & Williamson Tobacco Corp., 529 U. S. 120, 132
(2000). Rather, “[t]he meaning—or ambiguity—of certain
words or phrases may only become evident when placed in
context. . . . It is a ‘fundamental canon of statutory construc
tion that the words of a statute must be read in their context
and with a view to their place in the overall statutory
scheme.’ ” Id., at 132–133 (quoting Davis v. Michigan Dept.
of Treasury, 489 U. S. 803, 809 (1989)).
We must therefore read § 7(a)(2) of the ESA against the
statutory backdrop of the many mandatory agency directives
whose operation it would implicitly abrogate or repeal if it
were construed as broadly as the Ninth Circuit did below.
When § 7(a)(2) is read this way, we are left with a fundamen
tal ambiguity that is not resolved by the statutory text. An
agency cannot simultaneously obey the differing mandates
set forth in § 7(a)(2) of the ESA and § 402(b) of the CWA, and
consequently the statutory language—read in light of the
canon against implied repeals—does not itself provide clear
guidance as to which command must give way.
In this situation, it is appropriate to look to the implement
ing agency’s expert interpretation, which cabins § 7(a)(2)’s
application to “actions in which there is discretionary Fed
eral involvement or control.” 50 CFR § 402.03. This read
ing harmonizes the statutes by applying § 7(a)(2) to guide
agencies’ existing discretionary authority, but not reading it
to override express statutory mandates.
2
We conclude that this interpretation is reasonable in light
of the statute’s text and the overall statutory scheme, and
that it is therefore entitled to deference under Chevron.
Section 7(a)(2) requires that an agency “insure” that the ac

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tions it authorizes, funds, or carries out are not likely to jeop
ardize listed species or their habitats. To “insure” some
thing—as the court below recognized—means “ ‘[t]o make
certain, to secure, to guarantee (some thing, event, etc.).’ ”
420 F. 3d, at 963 (quoting 7 Oxford English Dictionary 1059
(2d ed. 1989)). The regulation’s focus on “discretionary” ac
tions accords with the commonsense conclusion that, when
an agency is required to do something by statute, it simply
lacks the power to “insure” that such action will not jeopar
dize endangered species.
This reasoning is supported by our decision in Department
of Transportation v. Public Citizen, 541 U. S. 752 (2004).
That case concerned safety regulations that were promul
gated by the Federal Motor Carrier Safety Administration
(FMCSA) and had the effect of triggering a Presidential di
rective allowing Mexican trucks to ply their trade on United
States roads. The Court held that the National Environ
mental Policy Act (NEPA) did not require the agency to as
sess the environmental effects of allowing the trucks entry
because “the legally relevant cause of the entry of the Mexi
can trucks is not FMCSA’s action, but instead the actions of
the President in lifting the moratorium and those of Con
gress in granting the President this authority while simulta
neously limiting FMCSA’s discretion.” Id., at 769 (emphasis
in original). The Court concluded that “where an agency
has no ability to prevent a certain effect due to its limited
statutory authority over the relevant actions, the agency
cannot be considered a legally relevant ‘cause’ of the effect.”
Id., at 770.
We do not suggest that Public Citizen controls the out
come here; § 7(a)(2), unlike NEPA, imposes a substantive
(and not just a procedural) statutory requirement, and these
cases involve agency action more directly related to environ
mental concerns than the FMCSA’s truck safety regulations.
But the basic principle announced in Public Citizen—that an

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agency cannot be considered the legal “cause” of an action
that it has no statutory discretion not to take—supports
the reasonableness of the FWS’ interpretation of § 7(a)(2)
as reaching only discretionary agency actions. See also
California v. United States, 438 U. S. 645, 668, n. 21 (1978)
(holding that a statutory requirement that federal operating
agencies conform to state water usage rules applied only
to the extent that it was not “inconsistent with other
congressional directives”).
3
The court below simply disregarded § 402.03’s interpreta
tion of the ESA’s reach, dismissing “the regulation’s refer
ence to ‘discretionary . . . involvement’ ” as merely “congru
ent with the statutory reference to actions ‘authorized,
funded, or carried out’ by the agency.” 420 F. 3d, at 968.
But this reading cannot be right. Agency discretion pre
sumes that an agency can exercise “judgment” in connection
with a particular action. See Citizens to Preserve Overton
Park, Inc. v. Volpe, 401 U. S. 402, 415–416 (1971); see also
Random House Dictionary of the English Language 411 (un
abridged ed. 1967) (“discretion” defined as “the power or
right to decide or act according to one’s own judgment; free
dom of judgment or choice”). As the mandatory language
of § 402(b) itself illustrates, not every action authorized,
funded, or carried out by a federal agency is a product of
that agency’s exercise of discretion.
The dissent’s interpretation of § 402.03 is similarly implau
sible. The dissent would read the regulation as simply clari
fying that discretionary agency actions are included within
the scope of § 7(a)(2), but not confining the statute’s reach to
such actions. See post, at 679–682. But this reading would
render the regulation entirely superfluous. Nothing in
either § 7(a)(2) or the other agency regulations interpreting
that section, see § 402.02, suggests that discretionary actions
are excluded from the scope of the ESA, and there is thus

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no need for a separate regulation to bring them within the
statute’s scope. On the dissent’s reading, § 402.03’s refer
ence to “discretionary” federal involvement is mere surplus
age, and we have cautioned against reading a text in a way
that makes part of it redundant. See, e. g., TRW Inc. v. An
drews, 534 U. S. 19, 31 (2001).
This history of the regulation also supports the reading to
which we defer today. As the dissent itself points out, the
proposed version of § 402.03 initially stated that “Section 7
and the requirements of this Part apply to all actions in
which there is Federal involvement or control,” 48 Fed. Reg.
29999 (1983) (emphasis added); the Secretary of the Interior
modified this language to provide (as adopted in the final
rule now at issue) that the statuory requirements apply to
“all actions in which there is discretionary Federal involve
ment or control,” 51 Fed. Reg. 19958 (1986) (emphasis added).
The dissent’s reading would rob the word “discretionary” of
any effect, and substitute the earlier, proposed version of the
regulation for the text that was actually adopted.
In short, we read § 402.03 to mean what it says: that
§ 7(a)(2)’s no-jeopardy duty covers only discretionary agency
actions and does not attach to actions (like the NPDES per
mitting transfer authorization) that an agency is required by
statute to undertake once certain specified triggering events
have occurred. This reading not only is reasonable, inas
much as it gives effect to the ESA’s provision, but also com
ports with the canon against implied repeals because it stays
§ 7(a)(2)’s mandate where it would effectively override other
wise mandatory statutory duties.
D
Respondents argue that our opinion in TVA v. Hill, 437
U. S. 153 (1978), supports their contrary position. In that
case, we held that the ESA prohibited the Tennessee Valley
Authority (TVA) from putting into operation the Tellico

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Dam—despite the fact that the agency had already spent
over $100 million on the nearly completed project—because
doing so would have threatened the critical habitat of the
endangered snail darter. In language on which respondents
rely, the Court concluded that “the ordinary meaning” of
§ 7 of the ESA contained “no exemptions” and reflected
“a conscious decision by Congress to give endangered species
priority over the ‘primary missions’ of federal agencies.”
Id., at 173, 185, 188.
TVA v. Hill, however, had no occasion to answer the ques
tion presented in these cases. That case was decided almost
a decade before the adoption in 1986 of the regulations con
tained in 50 CFR § 402.03. And in any event, the construc
tion project at issue in TVA v. Hill, while expensive, was
also discretionary. The TVA argued that by continuing to
make lump-sum appropriations to the TVA, some of which
were informally earmarked for the Tellico Dam project, Con
gress had implicitly repealed § 7’s no-jeopardy requirement
as it applied to that project. See 437 U. S., at 189–193. The
Court rejected this argument, concluding that “[t]he Appro
priations Acts did not themselves identify the projects for
which the sums had been appropriated” and that reports by
congressional committees allegedly directing the TVA to
complete the project lacked the force of law. Id., at 189,
n. 35. Central to the Court’s decision was the conclusion
that Congress did not mandate that the TVA put the dam
into operation; there was no statutory command to that ef
fect; and there was therefore no basis for contending that
applying the ESA’s no-jeopardy requirement would implic
itly repeal another affirmative congressional directive.9
9 The dissent is incorrect in suggesting that “if the Secretary of the
Interior had not declared the snail darter an endangered species . . . the
TVA surely would have been obligated to spend the additional funds that
Congress appropriated to complete the project.” Post, at 676. To the
contrary, the Court in TVA v. Hill found that there was no clear repug

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TVA v. Hill thus supports the position, expressed in
§ 402.03, that the ESA’s no-jeopardy mandate applies to
every discretionary agency action—regardless of the ex
pense or burden its application might impose. But that case
did not speak to the question whether § 7(a)(2) applies to
non-discretionary actions, like the one at issue here. The
regulation set forth in 50 CFR § 402.03 addressed that ques
tion, and we defer to its reasonable interpretation.
IV
Finally, respondents and their amici argue that, even if
§ 7(a)(2) is read to apply only to “discretionary” agency ac
tions, the decision to transfer NPDES permitting authority
to Arizona represented such an exercise of discretion. They
contend that the EPA’s decision to authorize a transfer is
not entirely mechanical; that it involves some exercise of
judgment as to whether a State has met the criteria set
forth in § 402(b); and that these criteria incorporate refer
ences to wildlife conservation that bring consideration of
§ 7(a)(2)’s no-jeopardy mandate properly within the Agen
cy’s discretion.
The argument is unavailing. While the EPA may exer
cise some judgment in determining whether a State has dem
onstrated that it has the authority to carry out § 402(b)’s
enumerated statutory criteria, the statute clearly does not
grant it the discretion to add another entirely separate pre
requisite to that list. Nothing in the text of § 402(b) au
thorizes the EPA to consider the protection of threatened
or endangered species as an end in itself when evaluating
a transfer application. And to the extent that some of the
§ 402(b) criteria may result in environmental benefits to ma
nancy between the ESA and the Acts appropriating funds to the TVA
because the latter simply did not require the agency to use any of the
generally appropriated funds to complete the Tellico Dam project. 437
U. S., at 189–193.

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rine species,10 there is no dispute that Arizona has satisfied
each of those statutory criteria.
Respondents’ argument has been disclaimed not only by
the EPA, but also by the FWS and the NMFS, the two agen
cies primarily charged with administering § 7(a)(2) and the
drafters of the regulations implementing that section. Each
agency recently issued a formal letter concluding that the
authorization of an NPDES permitting transfer is not the
kind of discretionary agency action that is covered by
§ 402.03. See App. to Pet. for Cert. in No. 06–549, at 103a–
116a. An agency’s interpretation of the meaning of its own
regulations is entitled to deference “unless plainly erroneous
or inconsistent with the regulation,” Auer v. Robbins, 519
U. S. 452, 461 (1997) (internal quotation marks omitted), and
that deferential standard is plainly met here.11
10 For example, § 402(b) requires the EPA to consider whether the State
has the legal authority to enforce applicable water quality standards—
some of which, in turn, are informed by the “judgment” of the EPA’s Ad
ministrator. 33 U. S. C. § 1342(b)(1)(A); see also, e. g., § 1312. But the
permit transfer process does not itself require scrutiny of the underlying
standards or of their effect on marine or wildlife—only of the state appli
cant’s “authority . . . [t]o issue permits which . . . apply, and insure compli
ance with,” the applicable standards. § 1342(b)(1)(A) (emphasis added).
In any event, respondents do not dispute that, as both the EPA and the
FWS determined, the transfer of permitting authority to Arizona officials
would have no adverse water quality related impact on any listed species.
See App. to Pet. for Cert. in No. 06–340, at 562–563, 615–617.
11 Respondents also contend that the EPA has taken, or will take, other
discretionary actions apart from the transfer authorization that implicate
the ESA. For example, they argue that the EPA’s alleged provision of
funding to Arizona for the administration of its clean water programs is
the kind of discretionary agency action that is subject to § 7(a)(2). How
ever, assuming this is true, any such funding decision is a separate agency
action that is outside the scope of this lawsuit. Respondents also point
to the fact that, following the transfer of permitting authority, the EPA
will retain oversight authority over the state permitting process, including
the power to object to proposed permits. But the fact that the EPA may
exercise discretionary oversight authority—which may trigger § 7(a)(2)’s

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* * *
Applying Chevron, we defer to the Agency’s reasonable
interpretation of ESA § 7(a)(2) as applying only to “actions in
which there is discretionary Federal involvement or control.”
50 CFR § 402.03. Since the transfer of NPDES permitting
authority is not discretionary, but rather is mandated once a
State has met the criteria set forth in § 402(b) of the CWA,
it follows that a transfer of NPDES permitting authority
does not trigger § 7(a)(2)’s consultation and no-jeopardy
requirements. Accordingly, the judgment of the Court of
Appeals for the Ninth Circuit is reversed, and these cases
are remanded for further proceedings consistent with this
opinion.
It is so ordered.
Justice Stevens, with whom Justice Souter, Justice
Ginsburg, and Justice Breyer join, dissenting.
These cases present a problem of conflicting “shalls.” On
the one hand, § 402(b) of the Clean Water Act (CWA) pro
vides that the Environmental Protection Agency (EPA)
“shall” approve a State’s application to administer a National
Pollution Discharge Elimination System (NPDES) permit
ting program unless it determines that nine criteria are not
satisfied. 33 U. S. C. § 1342(b). On the other hand, shortly
after the passage of the CWA, Congress enacted § 7(a)(2) of
the Endangered Species Act of 1973 (ESA), which commands
that federal agencies “shall” ensure that their actions do not
jeopardize endangered species. 16 U. S. C. § 1536(a)(2).
When faced with competing statutory mandates, it is our
duty to give full effect to both if at all possible. See, e. g.,
Morton v. Mancari, 417 U. S. 535, 551 (1974) (“[W]hen two
statutes are capable of co-existence, it is the duty of the
consultation and no-jeopardy obligations—after the transfer does not
mean that the decision authorizing the transfer is itself discretionary.

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courts, absent a clearly expressed congressional intention to
the contrary, to regard each as effective”). The Court fails
at this task. Its opinion unsuccessfully tries to reconcile the
CWA and the ESA by relying on a federal regulation, 50
CFR § 402.03 (2006), which it reads as limiting the reach of
§ 7(a)(2) to only discretionary federal actions, see ante, at
664–666. Not only is this reading inconsistent with the text
and history of § 402.03, but it is fundamentally inconsistent
with the ESA itself.
In the celebrated “snail darter” case, TVA v. Hill, 437 U. S.
153 (1978), we held that the ESA “reveals a conscious deci
sion by Congress to give endangered species priority over
the ‘primary missions’ of federal agencies,” id., at 185. Con
sistent with that intent, Chief Justice Burger’s exceptionally
thorough and admirable opinion explained that § 7 “admits
of no exception.” Id., at 173. Creating precisely such an
exception by exempting nondiscretionary federal actions
from the ESA’s coverage, the Court whittles away at Con
gress’ comprehensive effort to protect endangered species
from the risk of extinction and fails to give the ESA its in
tended effect. After first giving Hill the attention it de
serves, I will comment further on the irrelevance of § 402.03
to these cases and offer other available ways to give effect
to both the CWA and the ESA. Having done so, I conclude
by explaining why these cases should be remanded to EPA
for further proceedings.
I
In Hill, we were presented with two separate questions:
(1) whether the ESA required a court to enjoin the operation
of the nearly completed Tellico Dam and Reservoir Project
because the Secretary of the Interior had determined that
its operation would eradicate a small endangered fish known
as a snail darter; and (2) whether post-1973 congressional
appropriations for the completion of the Tellico Dam consti
tuted an implied repeal of the ESA, at least insofar as it

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applied to the dam. Id., at 156. More than 30 pages of our
opinion explain our affirmative answer to the first question,
see id., at 156–188, but just over four pages sufficed to ex
plain our negative answer to the second, see id., at 189–193.
While it is our ruling on the first question that is relevant to
the cases before us, it is our refusal to hold that the ESA
itself had been impliedly repealed that the majority
strangely deems most significant. See ante, at 670.
In answering Hill’s first question, we did not discuss im
plied repeals. On the contrary, that portion of the opinion
contained our definitive interpretation of the ESA, in which
we concluded that “the language, history, and structure of
the [ESA] indicates beyond doubt that Congress intended
endangered species to be afforded the highest of priorities.”
437 U. S., at 174; see also id., at 177 (“ ‘The dominant theme
pervading all Congressional discussion of the proposed
[ESA] was the overriding need to devote whatever effort and
resources were necessary to avoid further diminution of na
tional and worldwide wildlife resources’ ” (quoting Coggins,
Conserving Wildlife Resources: An Overview of the Endan
gered Species Act of 1973, 51 N. D. L. Rev. 315, 321 (1975);
emphasis added in Hill)). With respect to § 7 in particular,
our opinion could not have been any clearer. We plainly
held that it “admits of no exception.” 437 U. S., at 173 (em
phasis added).1
Our opinion in Hill explained at length why § 7 imposed
obligations on “all federal agencies” to ensure that “actions
authorized, funded, or carried out by them do not jeopardize
the continued existence of endangered species.” 437 U. S.,
1 See also Babbitt v. Sweet Home Chapter, Communities for Great Ore.,
515 U. S. 687, 692 (1995) (“Section 7 requires federal agencies to ensure
that none of their activities, including the granting of licenses and per
mits, will jeopardize the continued existence of endangered species ‘or
result in the destruction or adverse modification of habitat of such species
which is determined by the Secretary . . . to be critical’ ” (emphasis
added)).

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at 173 (emphasis deleted; internal quotation marks omitted).
Not a word in the opinion stated or suggested that § 7 obliga
tions are inapplicable to mandatory agency actions that
would threaten the eradication of an endangered species.
Nor did the opinion describe the Tennessee Valley Author
ity’s (TVA) attempted completion of the Tellico Dam as a
discretionary act. How could it? After all, if the Secretary
of the Interior had not declared the snail darter an endan
gered species whose critical habitat would be destroyed by
operation of the Tellico Dam, the TVA surely would have
been obligated to spend the additional funds that Congress
appropriated to complete the project.2 Unconcerned with
whether an agency action was mandatory or discretionary,
we simply held that § 7 of the ESA
“reveals an explicit congressional decision to require
agencies to afford first priority to the declared national
policy of saving endangered species. The pointed omis
sion of the type of qualifying language previously in
cluded in endangered species legislation reveals a con
scious decision by Congress to give endangered species
priority over the ‘primary missions’ of federal agen
cies.” Id., at 185 (emphasis added).3
2 The Court misreads this sentence and, in so doing, overreads our deci
sion in Hill. The Court maintains that Hill held that the “[a]cts appropri
ating funds to the TVA . . . did not require the agency to use any of the
generally appropriated funds to complete the Tellico Dam project.” Ante,
at 671, n. 9. But Hill said no such thing. That case only held that the
subsequent appropriation of funds for the Tellico Dam Project could not
overcome the mandatory requirements of § 7 of the ESA; it did not hold
that the TVA would not have been required to spend any and all appro
priated funds if the ESA had never been passed. See Hill, 437 U. S., at
189–190. If the ESA had never been enacted and did not stand in the
way of the completion of the Tellico Dam, there is no doubt that the TVA
would have finished the project that Congress had funded.
3 The road not taken in Hill also helps to clarify our interpretation that
§ 7 was not limited to discretionary agency action. Throughout the course
of the litigation, the TVA insisted that § 7 did not refer to “all the actions
that an agency can ever take.” Brief for Petitioner in Tennessee Valley

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The fact that we also concluded that the post-1973 congres
sional appropriations did not impliedly repeal the ESA pro
vides no support for the majority’s contention that the obli
gations imposed by § 7(a)(2) may be limited to discretionary
acts. A few passages from the relevant parts of Hill belie
that suggestion. After noting the oddity of holding that the
interest in protecting the survival of a relatively small num
ber of 3-inch fish “would require the permanent halting of a
virtually completed dam for which Congress has expended
more than $100 million,” we found “that the explicit provi
sions of the [ESA] require precisely that result.” Id., at 172,
173. We then continued:
“One would be hard pressed to find a statutory pro
vision whose terms were any plainer than those in § 7
of the [ESA]. Its very words affirmatively command
all federal agencies ‘to insure that actions authorized,
funded, or carried out by them do not jeopardize the
continued existence’ of an endangered species or ‘result
in the destruction or modification of habitat of such
species . . . .’ ” Id., at 173 (quoting 16 U. S. C. § 1536
(1976 ed.); emphasis added in Hill).
We also reviewed the ESA’s history to identify a variety of
exceptions that had been included in earlier legislation and
unenacted proposals but were omitted from the final version
of the 1973 statute. We explained that earlier endangered
species legislation “qualified the obligation of federal agen
cies,” but the 1973 Act purposefully omitted “all phrases
which might have qualified an agency’s responsibilities.”
437 U. S., at 181, 182. Moreover, after observing that the
Authority v. Hill, O. T. 1977, No. 76–1701, p. 26. Instead, the TVA sought
to restrict § 7 to only those actions for “which the agency has reasonable
decision-making alternatives before it.” Ibid. We rejected that narrow
interpretation, stating that the only way to sustain the TVA’s position
would be to “ignore the ordinary meaning of plain language.” Hill, 437
U. S., at 173.

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ESA creates only a limited number of “hardship exemp
tions,” see 16 U. S. C. § 1539—none of which would apply to
federal agencies—we applied the maxim expressio unius est
exclusio alterius to conclude that “there are no exemptions
in the [ESA] for federal agencies,” 437 U. S., at 188.
Today, however, the Court countenances such an exemp
tion. It erroneously concludes that the ESA contains an un
mentioned exception for nondiscretionary agency action and
that the statute’s command to enjoin the completion of the
Tellico Dam depended on the unmentioned fact that the TVA
was attempting to perform a discretionary act. But both
the text of the ESA and our opinion in Hill compel the con
trary determination that Congress intended the ESA to
apply to “all federal agencies” and to all “actions authorized,
funded, or carried out by them.” Id., at 173 (emphasis
deleted).
A transfer of NPDES permitting authority under § 402(b)
of the CWA is undoubtedly one of those “actions” that is
“authorized” or “carried out” by a federal agency. See 16
U. S. C. § 1536(b); 50 CFR § 402.02 (defining “action” as “all
activities or programs of any kind authorized, funded, or car
ried out, in whole or in part, by Federal agencies in the
United States or upon the high seas. Examples include, but
are not limited to . . . actions directly or indirectly causing
modifications to the land, water, or air”). It follows from
Hill that § 7(a)(2) applies to such NPDES transfers—
whether they are mandatory or discretionary.
II
Given our unequivocal holding in Hill that the ESA has
“first priority” over all other federal action, 437 U. S., at 185,
if any statute should yield, it should be the CWA. But no
statute must yield unless it is truly incapable of coexistence.
See, e. g., Morton, 417 U. S., at 551. Therefore, assuming
that § 402(b) of the CWA contains its own mandatory com

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mand, we should first try to harmonize that provision with
the mandatory requirements of § 7(a)(2) of the ESA.
The Court’s solution is to rely on 50 CFR § 402.03, which
states that “Section 7 and the requirements of this part
apply to all actions in which there is discretionary Federal
involvement or control.” The Court explains that this regu
lation “harmonizes the statutes by giving effect to the ESA’s
no-jeopardy mandate whenever an agency has discretion to
do so, but by lifting that mandate when the agency is prohib
ited from considering such extrastatutory factors.” Ante,
at 665. This is not harmony, and it certainly is not effect.
Rather than giving genuine effect to § 7(a)(2), the Court per
mits a wholesale limitation on the reach of the ESA. Its
interpretation of § 402.03 conflicts with the text and history
of the regulation, as well as our interpretation of § 7 in the
“snail darter” case.
To begin with, the plain language of § 402.03 does not state
that its coverage is limited to discretionary actions. Quite
the opposite, the most natural reading of the text is that it
confirms the broad construction of § 7 endorsed by our opin
ion in Hill. Indeed, the only way to read § 402.03 in accord
ance with the facts of the case and our holding that § 7 “ad
mits of no exception[s],” 437 U. S., at 173, is that it eliminates
any possible argument that the ESA does not extend to situ
ations in which the discretionary federal involvement is
only marginal.
The Court is simply mistaken when it says that it reads
§ 402.03 “to mean what it says: that § 7(a)(2)’s no-jeopardy
duty covers only discretionary agency actions . . . .” Ante,
at 669 (emphasis added). That is not, in fact, what § 402.03
“says.” The word “only” is the Court’s addition to the text,
not the Agency’s. Moreover, that text surely does not go on
to say (as the Court does) that the duty “does not attach to
actions (like the NPDES permitting transfer authorization)
that an agency is required by statute to undertake once cer

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tain specified triggering events have occurred.” Ibid. If
the drafters of the regulation had intended such a far
reaching change in the law, surely they would have said
so by using language similar to that which the Court uses
today.
Nothing in the proceedings that led to the promulgation of
the regulation suggests any reason for limiting the pre
existing understanding of the scope of § 7’s coverage. EPA
codified the current version of § 402.03 in 1986 as part of a
general redrafting of ESA regulations. In the 1983 Notice
of Proposed Rulemaking, the proposed version of § 402.03
stated that Ҥ 7 and the requirements of this Part apply to
all actions in which there is Federal involvement or control.”
48 Fed. Reg. 29999 (1983). Without any explanation, the
final rule inserted the word “discretionary” before “Federal
involvement or control.” 51 Fed. Reg. 19958 (1986).4
Clearly, if the Secretary of the Interior meant to limit the
pre-existing understanding of the scope of the coverage of
§ 7(a)(2) by promulgating this regulation, that intent would
have been mentioned somewhere in the text of the regula
tions or in contemporaneous comment about them. See Na
tional Cable & Telecommunications Assn. v. Brand X In
ternet Services, 545 U. S. 967, 1001 (2005) (holding that an
agency is free within “the limits of reasoned interpretation
to change course” only if it “adequately justifies the change”);
Motor Vehicle Mfrs. Assn. of United States, Inc. v. State
Farm Mut. Automobile Ins. Co., 463 U. S. 29, 48 (1983) (“We
have frequently reiterated that an agency must cogently ex
plain why it has exercised its discretion in a given manner”).
Yet, the final rule said nothing about limiting the reach of
4 See also Kilbourne, The Endangered Species Act Under the Micro
scope: A Closeup Look From A Litigator’s Perspective, 21 Env. L. 499,
529 (1991) (noting that the Agency did not explain the addition of the word
“discretionary”); Weller, Limiting the Scope of the Endangered Species
Act: Discretionary Federal Involvement or Control Under Section 402.03,
5 Hastings W.-Nw. J. Env. L. & Pol’y 309, 311, 334 (Spring 1999) (same).

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§ 7 or our decision in Hill. Nor did it mention the change
from the notice of proposed rulemaking. I can only assume,
then, that the regulation does mean what both it and the
notice of proposed rulemaking says: Section 7(a)(2) applies
to discretionary federal action, but not only to discretion
ary action.
The only explanation the Agency provided for § 402.03 was
the following:
“This section, which explains the applicability of section
7, implicitly covers Federal activities within the territo
rial jurisdiction of the United States and upon the high
seas as a result of the definition of ‘action’ in § 402.02.
The explanation for the scope of the term ‘action’ is pro
vided in the discussion under § 402.01 above.” 51 Fed.
Reg. 19937.
This statement directs us to two sources: the definition of
“action” in § 402.02 and the “explanation for the scope of the
term ‘action’ ” in § 402.01. 51 Fed. Reg. 19937. Both con
firm that there was no intent to draw a distinction between
discretionary and nondiscretionary actions.
Section 402.02 provides in relevant part:
“Action means all activities or programs of any kind
authorized, funded, or carried out, in whole or in part,
by Federal agencies in the United States or upon the
high seas. Examples include, but are not limited to:
“(a) actions intended to conserve listed species or
their habitat;
“(b) the promulgation of regulations . . . .” (Second
and third emphases added.)
Actions in either of the described subcategories are some
times mandatory and sometimes discretionary. Likewise, as
the italicized portions indicate, the term “action” expressly
refers to “all” agency activities or programs “of any kind,”
regardless of whether they are discretionary or mandatory.
By reading the term “discretionary” as a limitation on “ac

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tion, ” the Court creates a contradiction in EPA’s own
regulation.5
As for the final rule’s explanation for the scope of the term
“action” in § 402.01, that too is fully consistent with my inter
pretation of § 402.03. That explanation plainly states that
“all Federal actions including ‘conservations programs’ are
subject to the consultation requirements of section 7(a)(2) if
they ‘may affect’ listed species or their critical habitats.” 51
Fed. Reg. 19929 (emphasis added). The regulation does not
say all “discretionary” federal actions, nor does it evince an
intent to limit the scope of § 7(a)(2) in any way. Rather, it
just restates that the ESA applies to “all” federal actions,
just as the notice of proposed rulemaking did. This explana
tion of the scope of the word “action” is therefore a strong
indication that the Court’s reading of “discretionary” is con
trary to its intended meaning.
An even stronger indication is the fact that at no point in
the administrative proceedings in these cases did EPA even
mention it.6 As an initial matter, it is worth emphasizing
5 Petitioner National Association of Home Builders (NAHB) points to
the following language from the final rule as an indication that § 7 only
applies to discretionary action: “ ‘[A] Federal agency’s responsibility under
section 7(a)(2) permeates the full range of discretionary authority held by
that agency.’ ” Brief for Petitioners NAHB et al. 32 (quoting 51 Fed. Reg.
19937). However, that language is found in a different section of the final
rule—the section describing the definition of “ ‘[r]easonable and prudent
alternatives’ ” under 50 CFR § 402.02. When put in its proper context,
the cited language simply indicates that any “reasonable and prudent al
ternative” may involve the “maximum exercise of Federal agency author
ity when to do so is necessary, in the opinion of the Service, to avoid
jeopardy.” 51 Fed. Reg. 19937. If that is not enough, the quoted text
supports my reading of § 402.03 even on NAHB’s reading. By indicating
that an agency’s § 7(a)(2) responsibility “permeates the full range” of its
discretionary authority, EPA confirmed that the ESA covers all discretion
ary actions. Ibid.
6 EPA also did not rely on § 402.03 in the Court of Appeals. See 420
F. 3d 946, 968 (CA9 2005) (“EPA makes no argument that its transfer
decision was not a ‘discretionary’ one within the meaning of 50 CFR

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that even if EPA had relied on § 402.03, its interpretation of
the ESA would not be entitled to deference under Chevron
U. S. A. Inc. v. Natural Resources Defense Council, Inc., 467
U. S. 837 (1984), because it is not charged with administering
that statute, id., at 844 (“We have long recognized that con
siderable weight should be accorded to an executive depart
ment’s construction of a statutory scheme it is entrusted to
administer” (emphasis added)); Department of Treasury v.
FLRA, 837 F. 2d 1163, 1167 (CADC 1988) (“[W]hen an
agency interprets a statute other than that which it has been
entrusted to administer, its interpretation is not entitled to
deference”). The Departments of the Interior and Com
merce, not EPA, are charged with administering the ESA.
See Babbitt v. Sweet Home Chapter, Communities for Great
Ore., 515 U. S. 687, 703–704 (1995). And EPA has conceded
that the Department of the Interior’s biological opinion “did
not discuss 50 C. F. R. 402.03, and it did not address the
question whether the consultation that produced the [biolog
ical opinion] was required by the ESA.” Pet. for Cert. in
No. 06–549, p. 24; see App. 77–124 (never mentioning
§ 402.03). Left with this unfavorable administrative record,
EPA can only lean on the fact that the Department of
the Interior has recently “clarified” its position regarding
§ 402.03 in a different administrative proceeding. See Pet.
for Cert. in No. 06–549, at 24–25; id., at 26 (“The recent F[ish
and Wildlife Service (FWS)] and N[ational Marine Fisheries
Service] communications regarding Alaska’s pending trans
fer application reflect those agencies’ considered interpreta
tions . . . of [50 CFR §] 402.03”); App. to Pet. for Cert. in
No. 06–340, pp. 103–116; see also ante, at 660, n. 5. We have
long held, however, that courts may not affirm an agency
action on grounds other than those adopted by the agency in
§ 402.03. . . . We may not affirm the EPA’s transfer decision on grounds
not relied upon by the agency. . . . As the EPA evidently does not regard
§ 402.03 as excluding the transfer decision, we should not so interpret the
regulations”).

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the administrative proceedings. See SEC v. Chenery Corp.,
318 U. S. 80, 87 (1943). The majority ignores this hoary
principle of administrative law and substitutes a post hoc in
terpretation of § 7(a)(2) and § 402.03 for that of the relevant
agency. For that reason alone, these cases should be re
manded to the Agency. And for the other reasons I have
given, § 402.03 cannot be used to harmonize the CWA and
the ESA.
III
There are at least two ways in which the CWA and the
ESA can be given full effect without privileging one statute
over the other.
A
The text of § 7(a)(2) itself provides the first possible way
of reconciling that provision with § 402(b) of the CWA. The
subsection reads:
“Each Federal agency shall, in consultation with and
with the assistance of the Secretary, insure that any ac
tion authorized, funded, or carried out by such agency
(hereinafter in this section referred to as an ‘agency ac
tion’) is not likely to jeopardize the continued existence
of any endangered species or threatened species or re
sult in the destruction or adverse modification of habitat
of such species which is determined by the Secretary,
after consultation as appropriate with affected States,
to be critical, unless such agency has been granted an
exemption for such action by the Committee pursuant
to subsection (h) of this section.” 16 U. S. C. § 1536(a)(2)
(emphasis added).
The Court is certainly correct that the use of the word
“shall” in § 7(a)(2) imposes a mandatory requirement on the
federal agencies. See ante, at 662. It is also correct that
the ESA’s “mandate is to be carried out through consultation
and may require the agency to adopt an alternative course of
action.” Ibid. The Court is too quick to conclude, however,

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that this consultation requirement creates an irreconcilable
conflict between this provision and § 402(b) of the CWA. It
rushes to this flawed judgment because of a basic conceptual
error—an error that is revealed as early as the first para
graph of its opinion. Rather than attempting to find a way
to give effect to § 7(a)(2)’s consultation requirement, the
Court frames the question presented as “whether § 7(a)(2)
effectively operates as a tenth criterion on which the trans
fer of permitting power under the first statute must be con
ditioned. ” Ante, at 649. The Court is not alone in this.
The author of the Ninth Circuit opinion below also stated
that the ESA “adds one requirement to the list of considera
tions under the Clean Water Act permitting transfer provi
sion.” 450 F. 3d 394, 404, n. 2 (2006) (Berzon, J., concurring
in denial of rehearing en banc) (emphasis in original). But
while the ESA does mandate that the relevant agencies “con
sul[t]” with the Interior Department, that consultation proc
ess also provides a way for the agencies to give effect to
both statutes.
The first step in the statutory consultation process is to
identify whether any endangered species will be affected by
an agency action. An agency proposing a particular action,
such as an NPDES transfer, will typically ask the Secretary
of the Interior whether any listed species may be present in
the area of the proposed action and whether that action will
“affect” those species. See 16 U. S. C. § 1536(c). It is en
tirely possible that no listed species will be affected, and any
anticipated conflict between the ESA and another statute
will have been avoided at this threshold stage. If, however,
the Secretary determines that a proposed action may affect
an endangered species or its critical habitat, the agency must
formally consult with the Secretary. This consultation cul
minates in the issuance of a “biological opinion,” which “de
tail[s] how the agency action affects the species or its critical
habitat.” § 1536(b)(3)(A); see also 50 CFR § 402.14(h).
Even at this stage, it is still possible that formal consultation

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will reveal that the agency action will not jeopardize any
species. See, e. g., 63 Fed. Reg. 51198 (1998) (noting that
FWS rendered a “ ‘no jeopardy’ ” finding with respect to the
transfer of permitting authority to Texas).
If the biological opinion concludes that the agency action
would put a listed species in jeopardy, however, the ESA
contains a process for resolving the competing demands of
agency action and species protection. The ESA provides
that “the Secretary shall suggest those reasonable and pru
dent alternatives which he believes would not violate sub
section (a)(2) and can be taken by the Federal agency or
applicant in implementing the agency action.” 16 U. S. C.
§ 1536(b)(3)(A); see also 50 CFR § 402.14(h)(3). EPA’s regu
lations define “[r]easonable and prudent alternatives” as
“alternative actions identified during formal consulta
tion that can be implemented in a manner consistent
with the intended purpose of the action, that can be
implemented consistent with the scope of the Federal
agency’s legal authority and jurisdiction, that is econom
ically and technologically feasible, and that the Director
[of FWS] believes would avoid the likelihood of jeopard
izing the continued existence of listed species or result
ing in the destruction or adverse modification of critical
habitat.” § 402.02.
Thus, in the face of any conflict between the ESA and an
other federal statute, the ESA and its implementing regula
tions encourage federal agencies to work out a reasonable
alternative that would let the proposed action move forward
“consistent with [its] intended purpose” and the agency’s
“legal authority,” while also avoiding any violation of
§ 7(a)(2).
When applied to the NPDES transfer program, the “rea
sonable and prudent alternatives” process would enable EPA
and the Department of the Interior to develop a substitute
that would allow a transfer of permitting authority and
would not jeopardize endangered species. Stated differ

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ently, the consultation process would generate an alternative
course of action whereby the transfer could still take place—
as required by § 402(b) of the CWA—but in such a way that
would honor the mandatory requirements of § 7(a)(2) of the
ESA. This should come as no surprise to EPA, as it has
engaged in pretransfer consultations at least six times in the
past and has stated that it is not barred from doing so by
the CWA.7
Finally, for the rare case in which no “reasonable and pru
dent alternative” can be found, Congress has provided yet
another mechanism for resolving any conflicts between the
ESA and a proposed agency action. In 1978, shortly after
our decision in Hill, Congress amended the ESA to create
the “Endangered Species Committee,” which it authorized to
grant exemptions from § 7(a)(2). 16 U. S. C. § 1536(e). Be
cause it has the authority to approve the extinction of an
endangered species, the Endangered Species Committee is
colloquially described as the “God Squad” or “God Commit
tee.” In light of this weighty responsibility, Congress care
fully laid out requirements for the God Committee’s mem
bership,8 procedures,9 and the factors it must consider in
deciding whether to grant an exemption.10
7 See, e. g., 63 Fed. Reg. 51198 (1998) (approving Texas’ application to
administer the NPDES program after consultation with FWS and stating
that “EPA believes that section 7 does apply” to EPA’s action); 61 Fed.
Reg. 65053 (1996) (approving Oklahoma’s NPDES application after consul
tation with FWS and stating that “EPA’s approval of the State permitting
program under section 402 of the Clear Water Act is a federal action
subject to [§ 7’s consultation] requirement”); see also Tr. of Oral Arg. 5
(conceding that EPA conducted six pretransfer consultations in the past).
8 The Endangered Species Committee is composed of six high-ranking
federal officials and a representative from each affected State appointed
by the President. See 16 U. S. C. § 1536(e)(3).
9 See §§ 1536(e)–(l).
10 Section 1536(h)(1) provides:
“The Committee shall grant an exemption from the requirements of
subsection (a)(2) of this section for an agency action if, by a vote of not
less than five of its members voting in person—

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As the final arbiter in situations in which the ESA conflicts
with a proposed agency action, the God Committee embodies
the primacy of the ESA’s mandate and serves as the final
mechanism for harmonizing that Act with other federal stat
utes. By creating this Committee, Congress recognized
that some conflicts with the ESA may not be capable of reso
lution without having to forever sacrifice some endangered
species. At the same time, the creation of this last line of
defense reflects Congress’ view that the ESA should not
yield to another federal action except as a final resort and
except when authorized by high-level officials after serious
consideration. In short, when all else has failed and two
federal statutes are incapable of resolution, Congress left the
choice to the Committee—not to this Court; it did not limit
the ESA in the way the majority does today.
B
EPA’s regulations offer a second way to harmonize the
CWA with the ESA. After EPA has transferred NPDES
permitting authority to a State, the Agency continues to
“(A) it determines on the record, based on the report of the Secretary,
the record of the hearing held under subsection (g)(4) and on such other
testimony or evidence as it may receive, that—
“(i) there are no reasonable and prudent alternatives to the agency
action;
“(ii) the benefits of such action clearly outweigh the benefits of alterna
tive courses of action consistent with conserving the species or its critical
habitat, and such action is in the public interest;
“(iii) the action is of regional or national significance; and
“(iv) neither the Federal agency concerned nor the exemption applicant
made any irreversible or irretrievable commitment of resources prohibited
by subsection (d) of this section; and
“(B) it establishes such reasonable mitigation and enhancement meas
ures, including, but not limited to, live propagation, transplantation, and
habitat acquisition and improvement, as are necessary and appropriate to
minimize the adverse effects of the agency action upon the endangered
species, threatened species, or critical habitat concerned.”

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oversee the State’s permitting program. See Arkansas v.
Oklahoma, 503 U. S. 91, 105 (1992) (“Congress preserved for
the Administrator broad authority to oversee state permit
programs”). If a state permit is “outside the guidelines and
the requirements” of the CWA, EPA may object to it and
block its issuance. See 33 U. S. C. § 1342(d)(2); 66 Fed. Reg.
11206 (2001). Given these ongoing responsibilities, EPA
has enacted a regulation that requires a State to enter into
a Memorandum of Agreement (MOA) that sets forth the
particulars of the Agency’s oversight duties. See 40 CFR
§ 123.24(a) (2006).
The regulation governing MOAs contains several detailed
requirements. For instance, the regulation states that an
MOA must contain “[p]rovisions specifying classes and cate
gories of permit applications, draft permits and proposed
permits that the State will send to the [EPA] Regional Ad
ministrator for review, comment and, where applicable, ob
jection,” § 123.24(b)(2); “[p]rovisions specifying the frequency
and content of reports, documents and other information
which the State is required to submit to the EPA,”
§ 123.24(b)(3); and “[p]rovisions for coordination of compli
ance monitoring activities by the State and by EPA,”
§ 123.24(b)(4)(i). More generally, the regulation provides
that an MOA “may include other terms, conditions, or agree
ments” that are “relevant to the administration and en
forcement of the State’s regulatory program.” § 123.24(a).
Under the MOA regulation, furthermore, EPA will not ap
prove any MOA that restricts its statutory oversight respon
sibility. Ibid.
Like the § 7(a)(2) consultation process described above,
MOAs provide a potential mechanism for giving effect to § 7
of the ESA while also allowing the transfer of permitting
authority to a State. It is important to remember that EPA
must approve an MOA prior to the transfer of NPDES au
thority. As such, EPA can use—and in fact has used—the
MOA process to structure its later oversight in a way that

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will allow it to protect endangered species in accordance
with § 7(a)(2) of the ESA. EPA might negotiate a provision
in the MOA that would require a State to abide by the ESA
requirements when issuing pollution permits. See Brief for
American Fisheries Society et al. as Amici Curiae 28 (“In
the Maine MOA, for example, EPA and the state agree that
state permits would protect ESA-listed species by ensuring
compliance with state water quality standards”). Alterna
tively, “EPA could require the state to provide copies of
draft permits for discharges in particularly sensitive habitats
such as those of ESA-listed species or for discharges that
contain a pollutant that threatens ESA-listed wildlife.” Id.,
at 10. Or the MOA might be drafted in a way that would
allow the agency to object to state permits that would jeop
ardize any and all endangered species. See id., at 28 (ex
plaining that the Maine MOA includes a provision allowing
EPA to “object to any state permit that risks harm to a
listed species by threatening water quality”). These are
just three of many possibilities. I need not identify other
ways EPA could use the MOA process to comply with the
ESA; it is enough to observe that MOAs provide a straight
forward way to give the ESA its full effect without restrict
ing § 7(a)(2) in the way the Court does.
IV
As discussed above, I believe that the Court incorrectly
restricts the reach of § 7(a)(2) to discretionary federal
actions. See Part II, supra. Even if such a limitation
were permissible, however, it is clear that EPA’s author
ity to transfer permitting authority under § 402(b) is
discretionary.11
The EPA Administrator’s authority to approve state per
mit programs pursuant to § 402(b) of the CWA does not even
fit within the Court’s description of the category of manda
11 Because it is quite lengthy, I include the full text of § 402(b) in an
appendix to this dissent.

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tory actions that the Court holds are covered by the ESA.
In the Court’s words, that category includes actions “that
an agency is required by statute to undertake once certain
specified triggering events have occurred.” Ante, at 669.
The “triggering event” for EPA’s approval is simply the fil
ing of a satisfactory description of the State’s proposed pro
gram. See 33 U. S. C. § 1342(b). The statute then com
mands that the EPA Administrator “shall approve” the
submitted program unless he determines that state law does
not satisfy nine specified conditions. Those conditions are
not “triggering events”; they are potential objections to the
exercise of the Administrator’s authority.
What is more, § 402(b) is a perfect example of why our
analysis should not end simply because a statute uses the
word “shall.” Instead, we must look more closely at its
listed criteria to determine whether they allow for discre
tion, despite the use of “shall.” After all, as then-Justice
Rehnquist’s dissenting opinion in the “snail darter” case ex
plains, a federal statute using the word “shall” will some
times allow room for discretion. See Hill, 437 U. S., at 211–
212.12 In these cases, there is significant room for discretion
in EPA’s evaluation of § 402(b)’s nine conditions. The first
criterion, for example, requires the EPA Administrator
to examine five other statutes and ensure that the State
has adequate authority to comply with each. 33 U. S. C.
§ 1342(b)(1)(A). One of those five statutes, in turn, ex
pressly directs the Administrator to exercise his “judgment.”
§ 1312. Even the Court acknowledges that EPA must exer
12 See Gutierrez de Martinez v. Lamagno, 515 U. S. 417, 432–433, n. 9
(1995) (“Though ‘shall’ generally means ‘must,’ legal writers sometimes
use, or misuse, ‘shall’ to mean ‘should,’ ‘will,’ or even ‘may.’ See D. Mellin
koff, Mellinkoff ’s Dictionary of American Legal Usage 402–403 (1992)
(‘shall’ and ‘may’ are ‘frequently treated as synonyms’ and their meaning
depends on context); B. Garner, Dictionary of Modern Legal Usage 939
(2d ed. 1995) (‘Courts in virtually every English-speaking jurisdiction have
held—by necessity—that shall means may in some contexts, and vice
versa’)”).

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cise “some judgment in determining whether a State has
demonstrated that it has the authority to carry out § 402(b)’s
enumerated statutory criteria.” Ante, at 671. However, in
the very same breath, the Court states that the dispositive
fact is that “the statute clearly does not grant it the discre
tion to add another entirely separate prerequisite to that
list.” Ibid. This reasoning flouts the Court’s own logic.
Under the Court’s reading of § 402.03, § 7(a)(2) applies to dis
cretionary federal actions of any kind. The Court plainly
acknowledges that EPA exercises discretion when deciding
whether to transfer permitting authority to a State. If we
are to take the Court’s approach seriously, once any dis
cretion has been identified—as it has here—§ 7(a)(2) must
apply.13
13 The Court also claims that the “basic principle announced in” Depart
ment of Transportation v. Public Citizen, 541 U. S. 752 (2004)—“that an
agency cannot be considered the legal ‘cause’ of an action that it has no
statutory discretion not to take”—supports its reliance on § 402.03. Ante,
at 667–668. First of all, the Court itself recognizes that it must distance
itself from that case, ante, at 667, because Public Citizen dealt with a
procedural requirement under the National Environmental Policy Act
(NEPA), not a substantive requirement like that imposed by § 7(a)(2) of
the ESA, see TVA v. Hill, 437 U. S. 153, 188, n. 34 (1978) (holding that
NEPA cases are “completely inapposite” to the ESA context). What the
Court does not recognize, however, is that what it views as the “basic
principle” of Public Citizen is stated too broadly and therefore inapplica
ble to these cases. Ante, at 667–668.
Our decision in Public Citizen turned on what we called “a critical fea
ture of the case”: that the Federal Motor Carrier Safety Administration
(FMCSA) had “no ability to countermand” the President’s lifting a morato
rium that prohibited certain motor carriers from obtaining authority to
operate within the United States. 541 U. S., at 766. Once the President
decided to lift that moratorium, and once the relevant vehicles had entered
the United States, FMCSA was required by statute to register the vehi
cles if certain conditions were met. Ibid. (“Under FMCSA’s entirely rea
sonable reading of this provision, it must certify any motor carrier that
can show that it is willing and able to comply with the various substantive
requirements for safety and financial responsibility contained in Depart

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Stevens, J., dissenting
The MOA regulation described in Part III–B, supra, also
demonstrates that an NPDES transfer is not as ministerial
a task as the Court would suggest. The Agency retains sig
nificant discretion under § 123.24 over the content of an
MOA, which of course must be approved prior to a transfer.
For instance, EPA may require a State to file reports on a
weekly basis or a monthly basis. It may require a State to
submit only certain classes and categories of permit applica
tions. And it may include any additional terms and condi
tions that are relevant to the enforcement of the NPDES
program. There is ample room for judgment in all of these
areas, and EPA has exercised such judgment in the past
when approving MOAs from many States. See, e. g., Ap
proval of Application by Maine to Administer the NPDES
Program, 66 Fed. Reg. 12791 (2001); Approval of Application
to Administer the NPDES Program; Texas, 63 Fed. Reg.
51164 (1998).
In fact, in an earlier case raising a question similar to this
one, see American Forest & Paper Assn. v. EPA, 137 F. 3d
291, 298–299 (CA5 1998), EPA itself explained how 40 CFR
§ 123.24 gives it discretion over the approval of a state pollu
tion control program, see Brief for EPA in No. 96–60874
(CA5). Arguing that “[i]ndicia of discretionary involvement
or control abound in [its] regulations,” the Agency listed
ment of Transportation regulations; only the moratorium prevented it
from doing so for Mexican motor carriers before 2001” (emphasis deleted)).
Therefore, any potential NEPA concerns were generated by another deci
sionmaker, the President, and not FMCSA. Here, by contrast, EPA is
not required to act ministerially once another person or agency has made
a decision. Instead, EPA must exercise its own judgment when consider
ing the transfer of NPDES authority to a State; it also has its own author
ity to deny such a transfer. Any effect on endangered species will be
caused, even if indirectly, by the Agency’s own decision to transfer
NPDES authority. Cf. 50 CFR § 402.02(d) (providing that the ESA will
apply to all agency activities that “directly or indirectly caus[e] modifica
tions to the land, water, or air” (emphasis added)).

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its MOA regulation as a prime example.14 Again, because
EPA’s approval of a state application to administer an
NPDES program entails significant—indeed, abounding—
discretion, I would find that § 7(a)(2) of the ESA applies even
under the Court’s own flawed theory of these cases.
V
Mindful that judges must always remain faithful to the
intent of the legislature, Chief Justice Burger closed his opin
ion in the “snail darter” case with a reminder that “[o]nce
the meaning of an enactment is discerned and its constitu
tionality determined, the judicial process comes to an end.”
Hill, 437 U. S., at 194. This Court offered a definitive inter
pretation of the ESA nearly 30 years ago in that very case.
Today the Court turns its back on our decision in Hill and
places a great number of endangered species in jeopardy, in
cluding the cactus ferruginous pygmy-owl and Pima pine
apple cactus at issue here. At the risk of plagiarizing Chief
Justice Burger’s fine opinion, I think it is appropriate to end
my opinion just as he did—with a quotation attributed to Sir
Thomas More that has as much relevance today as it did
three decades ago. This quotation illustrates not only the
fundamental character of the rule of law embodied in § 7 of
the ESA but also the pernicious consequences of official dis
obedience of such a rule. Repetition of that literary allusion
is especially appropriate today:
“The law, Roper, the law. I know what’s legal, not
what’s right. And I’ll stick to what’s legal. . . . I’m not
God. The currents and eddies of right and wrong,
14 EPA also discussed several other regulations that give it discretion.
For example, under 40 CFR § 123.61(b), EPA is required to solicit public
comments on a State’s transfer application, and it must “approve or disap
prove the program” after “taking into consideration all comments re
ceived.” As EPA explained in its Fifth Circuit brief, if it “were simply
acting in a ministerial fashion, such weighing of the merits of public com
ments would be unnecessary.” Brief for EPA in No. 96–60874 (CA5).

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which you find such plain-sailing, I can’t navigate, I’m
no voyager. But in the thickets of the law, oh there I’m
a forester. . . . What would you do? Cut a great road
through the law to get after the Devil? . . . And when
the last law was down, and the Devil turned round on
you—where would you hide, Roper, the laws all being
flat? . . . This country’s planted thick with laws from
coast to coast—Man’s laws, not God’s—and if you cut
them down . . . d’you really think you could stand up
right in the winds that would blow then? . . . Yes, I’d
give the Devil benefit of law, for my own safety’s sake.”
R. Bolt, A Man for All Seasons, Act I, p. 147 (Three
Plays, Heinemann ed. 1967) (quoted in Hill, 437 U. S.,
at 195).
Although its reasons have shifted over time, at both the
administrative level and in the federal courts, EPA has in
sisted that the requirements of § 7(a)(2) of the ESA do not
apply to its decision to transfer permitting authority under
§ 402(b) of the CWA. See App. 114; Brief for Petitioner
EPA 16, 42. As I have explained above, that conclusion is
contrary to the text of § 7(a)(2), our decision in TVA v. Hill,
and the regulation on which the Agency has since relied and
upon which the Court relies today. Accordingly, I would
hold that EPA’s decision was arbitrary and capricious under
the Administrative Procedure Act, see 5 U. S. C. § 706(2)(A),
and would remand to the Agency for further proceedings
consistent with this opinion.
I respectfully dissent.
APPENDIX
33 U. S. C. § 1342(b)
“(b) State permit programs
“At any time after the promulgation of the guidelines re
quired by subsection (i)(2) of section 1314 of this title, the
Governor of each State desiring to administer its own permit

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program for discharges into navigable waters within its ju
risdiction may submit to the Administrator a full and com
plete description of the program it proposes to establish and
administer under State law or under an interstate compact.
In addition, such State shall submit a statement from the
attorney general (or the attorney for those State water pollu
tion control agencies which have independent legal counsel),
or from the chief legal officer in the case of an interstate
agency, that the laws of such State, or the interstate com
pact, as the case may be, provide adequate authority to carry
out the described program. The Administrator shall ap
prove each submitted program unless he determines that ad
equate authority does not exist:
“(1) To issue permits which—
“(A) apply, and insure compliance with, any applicable re
quirements of sections 1311, 1312, 1316, 1317, and 1343 of
this title;
“(B) are for fixed terms not exceeding five years; and
“(C) can be terminated or modified for cause including, but
not limited to, the following:
“(i) violation of any condition of the permit;
“(ii) obtaining a permit by misrepresentation, or failure to
disclose fully all relevant facts;
“(iii) change in any condition that requires either a tempo
rary or permanent reduction or elimination of the permit
ted discharge;
“(D) control the disposal of pollutants into wells;
“(2)(A) To issue permits which apply, and insure compli
ance with, all applicable requirements of section 1318 of this
title; or
“(B) To inspect, monitor, enter, and require reports to at
least the same extent as required in section 1318 of this title;
“(3) To insure that the public, and any other State the wa
ters of which may be affected, receive notice of each applica
tion for a permit and to provide an opportunity for public
hearing before a ruling on each such application;

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697 Cite as: 551 U. S. 644 (2007)
Appendix to opinion of Stevens, J.
“(4) To insure that the Administrator receives notice of
each application (including a copy thereof) for a permit;
“(5) To insure that any State (other than the permitting
State), whose waters may be affected by the issuance of
a permit may submit written recommendations to the per
mitting State (and the Administrator) with respect to any
permit application and, if any part of such written recom
mendations are not accepted by the permitting State, that
the permitting State will notify such affected State (and the
Administrator) in writing of its failure to so accept such rec
ommendations together with its reasons for so doing;
“(6) To insure that no permit will be issued if, in the judg
ment of the Secretary of the Army acting through the Chief
of Engineers, after consultation with the Secretary of the
department in which the Coast Guard is operating, anchor
age and navigation of any of the navigable waters would be
substantially impaired thereby;
“(7) To abate violations of the permit or the permit pro
gram, including civil and criminal penalties and other ways
and means of enforcement;
“(8) To insure that any permit for a discharge from a pub
licly owned treatment works includes conditions to require
the identification in terms of character and volume of pollut
ants of any significant source introducing pollutants subject
to pretreatment standards under section 1317(b) of this title
into such works and a program to assure compliance with
such pretreatment standards by each such source, in addition
to adequate notice to the permitting agency of (A) new intro
ductions into such works of pollutants from any source which
would be a new source as defined in section 1316 of this title
if such source were discharging pollutants, (B) new introduc
tions of pollutants into such works from a source which
would be subject to section 1311 of this title if it were dis
charging such pollutants, or (C) a substantial change in vol
ume or character of pollutants being introduced into such
works by a source introducing pollutants into such works at

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Breyer, J., dissenting
the time of issuance of the permit. Such notice shall include
information on the quality and quantity of effluent to be in
troduced into such treatment works and any anticipated im
pact of such change in the quantity or quality of effluent to be
discharged from such publicly owned treatment works; and
“(9) To insure that any industrial user of any publicly
owned treatment works will comply with sections 1284(b),
1317, and 1318 of this title.”
Justice Breyer, dissenting.
I join Justice Stevens’ dissent, while reserving judg
ment as to whether § 7(a)(2) of the Endangered Species Act
of 1973, 16 U. S. C. § 1536(a)(2), really covers every possible
agency action even of totally unrelated agencies—such as,
say, a discretionary determination by the Internal Revenue
Service whether to prosecute or settle a particular tax liabil
ity, see 26 U. S. C. § 7121.
At the same time I add one additional consideration in sup
port of his (and my own) dissenting views. The Court em
phasizes that “[b]y its terms, the statutory language [of
§ 402(b) of the Clean Water Act, 33 U. S. C. § 1342(b),] is man
datory and the list exclusive; if the nine specified criteria are
satisfied, the EPA does not have the discretion to deny a
transfer application.” Ante, at 661 (emphasis added). My
own understanding of agency action leads me to believe that
the majority cannot possibly be correct in concluding that
the structure of § 402(b) precludes application of § 7(a)(2) to
the EPA’s discretionary action. See ante, at 690–692 (Ste
vens, J., dissenting). That is because grants of discre
tionary authority always come with some implicit limits
attached. See L. Jaffe, Judicial Control of Administrative
Action 359 (1965) (discretion is “a power to make a choice”
from a “permissible class of actions”). And there are likely
numerous instances in which, prior to, but not after, the en
actment of § 7(a)(2), the statute might have implicitly placed
“species preservation” outside those limits.

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Breyer, J., dissenting
To take one example, consider the statute that once
granted the old Federal Power Commission (FPC) the au
thority to grant a “certificate of public convenience and
necessity” to permit a natural gas company to operate a
new pipeline. See 15 U. S. C. § 717f(c)(1)(A). It says that
“a certificate shall be issued to any qualified applicant
therefor . . . if it is found that the applicant is able and will
ing properly to do the acts and to perform the service
proposed . . . and that the proposed service . . . is or will
be required by the present or future public convenience and
necessity.” § 717f(e).
Before enactment of the Endangered Species Act of 1973,
87 Stat. 884, it is at least uncertain whether the FPC could
have withheld a certificate simply because a natural gas pipe
line might threaten an endangered animal, for given the
Act’s language and history, species preservation does not
naturally fall within its terms. But we have held that the
Endangered Species Act changed the regulatory landscape,
“indicat[ing] beyond doubt that Congress intended endan
gered species to be afforded the highest of priorities.” TVA
v. Hill, 437 U. S. 153, 174 (1978) (emphasis added). Indeed,
the Endangered Species Act demonstrated “a conscious deci
sion by Congress to give endangered species priority over
the ‘primary missions’ of federal agencies.” Id., at 185.
And given a new pipeline’s potential effect upon habitat and
landscape, it seems reasonable to believe, once Congress
enacted the new law, the FPC’s successor (the Federal En
ergy Regulatory Commission) would act within its authority
in taking species-endangering effects into account.
To take another example, the Food and Drug Administra
tion (FDA) has, by statute, an “exclusive” list of criteria to
consider in reviewing applications for approval of a new
drug. See 21 U. S. C. § 355(d) (“If the Secretary finds . . .
[e. g.,] the investigations . . . do not include adequate tests
by all methods reasonably applicable to show whether or not
such drug is safe . . . he shall issue an order refusing to

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approve the application”). Preservation of endangered spe
cies is not on this “exclusive” list of criteria. Yet I imagine
that the FDA now should take account, when it grants or
denies drug approval, of the effect of manufacture and mar
keting of a new drug upon the preservation or destruction
of an endangered species.
The only meaningful difference between the provision now
before us, § 402(b) of the Clean Water Act, and the energy
and drug-related statutes that I have mentioned is that the
very purpose of the former is to preserve the state of our
natural environment—a purpose that the Endangered Spe
cies Act shares. That shared purpose shows that § 7(a)(2)
must apply to the Clean Water Act a fortiori.