rule appropriately balanced the scope of State authority under section
401 with Congress' goal of facilitating commerce on interstate
navigable waters. Some commenters argued that the cases referenced in
the proposed rule preamble, including Lighthouse Resources, Inc. v.
Inslee and Lake Carrier's Association v. EPA, 652 F.3d 1 (D.C. Cir.
2011), are not relevant to this rulemaking. The Agency disagrees with
the suggestion that these cases are irrelevant because, among other
things, they demonstrate that section 401

actions are not insulated from legal challenges asserting State or
Tribal interference with interstate commerce and violations of the
Commerce Clause. The Agency did not rely on these decisions to inform
the substance of the final rule; rather, they were considered as part
of the overall context of litigation and regulatory uncertainty that
contributed to the need to update the 1971 certification regulations to
be consistent with CWA section 401.
    Other commenters supported the proposal and raised concerns that
States and Tribes could use section 401 actions to override federal
trade policy with which they disagree. At least one commenter asserted
that coastal States and States that border Canada and Mexico could
misuse section 401 to block the construction of international terminals
for exports, including energy, agricultural, and manufacturing exports.
This commenter asserted that such misuse could also result in blocking
imports from trading partners based on objections of a single State.
The EPA appreciates these comments and agrees that there is a risk that
State or Tribal certification authority could be misused in the way
described by the commenter. However, as described elsewhere in this
final rule preamble and in the Economic Analysis for the Clean Water
Act Section 401 Certification Rule (``the Economic Analysis,''
available in the docket for this final rule), the EPA acknowledges that
many certifications reflect an appropriately limited interpretation of
the purpose and scope of section 401 and are issued without
controversy, and that the limitations expressed in this rulemaking
should further curb any improper invocation of section 401 authority.
    The EPA has determined that this final rule appropriately balances
the interests of State or Tribal participation in federal license or
permit proceedings under section 401 with Congress' goal of
facilitating interstate commerce on navigable waters. Because Congress
relied on its authority under the Interstate Commerce Clause when it
enacted the CWA, including section 401, this rule respects that
balance. The Agency has for the first time clearly defined the scope of
certification, reducing the risk that States and Tribes would deny or
condition certifications for reasons beyond the authority provided in
section 401 or that such denials or conditions would place undue
burdens on interstate commerce.
b. Cooperative Federalism
    A number of commenters asserted that the proposed rule is
inconsistent with the concept of cooperative federalism and the
important role of States and Tribes as co-regulators, and therefore,
these commenters believed that the proposed rule undermines the
cooperative federalism structure established by Congress in the CWA in
section 101(b) and section 101(g). Most of these commenters noted that
the CWA recognizes States' primary authority over their water
resources, designates States as co-regulators under a system of
cooperative federalism, and expresses intent to preserve and protect
States' responsibilities and rights. Commenters stated that the CWA was
founded on a principle of cooperative federalism, and that the EPA
should not dictate what States can and cannot do. Another commenter
asserted that the proposed rule would unduly limit States' authority
and autonomy to protect their water resources. A few commenters
asserted that the proposed rule would harm Congress' division of
authority between certifying authorities and federal licensing and
permitting agencies. Some commenters asserted that the proposed rule
neglects States' interests.
    Other commenters asserted that the proposed rule is consistent with
the overall cooperative federalism framework established by Congress in
the CWA and appropriately balances federal and State authority. A few
commenters argued that under section 401, Congress was conferring on
States a narrow exception to act in areas that are otherwise preempted
entirely by federal law. These commenters described section 401
certifications as playing a limited role in a much larger federal
permitting scheme envisioned in the CWA. A few commenters supporting
the proposed rule described an appreciation for the EPA's desire to
preserve State sovereignty and cooperative federalism in conjunction
with greater consistency in implementing section 401. Several
commenters observed that the proposed rule would promote efficiency and
would be consistent with the intent of the 1972 CWA amendments, leading
to consistent nationwide implementation, while allowing the States to
retain their primary roles under the CWA. Other commenters stated that
the current regulations have allowed States to impose conditions beyond
the scope of water quality effects of a discharge, leading to lengthy
delays and a process that is ill-defined, confusing in scope, and
lacking clear deadlines. Other commenters suggested that the proposed
rule supports timely issuance of permits and licenses and agreed that
the proposed rule would ensure that section 401 certification does not
exceed the scope of CWA jurisdiction.
    The EPA has considered these diverse comments and concludes that
the final rule does not infringe upon the roles of States as co-
regulators, nor does it undermine cooperative federalism. The final
rule does not and cannot alter the basic scope of authority granted by
Congress to States and Tribes for the review of potential discharges
associated with federal licenses and permits for compliance with water
quality standards. States and authorized Tribes, for example, remain
primarily responsible to develop the water quality standards with which
federal projects must comply.
    Accordingly, this rule neither diminishes nor undermines
cooperative federalism. Rather, the final rule clearly identifies when
a certification is required and the permissible scope of such a
certification--including conditions of that certification--and
reaffirms that certifying authorities have a reasonable period of time
to act on a certification request, which cannot exceed one year. This
clarity helps define the appropriate parameters of cooperative
federalism contemplated by section 401, and does not undermine it.
    The EPA disagrees with commenters who suggest that concepts of
``cooperative federalism'' preclude the EPA from establishing
regulations to implement section 401. Cooperative federalism must be
implemented consistent with the statutory framework under the CWA,
which does not allow EPA to authorize, either explicitly or by
implication, States to implement this important federal program in a
manner beyond the authority established by Congress. Indeed, as the
Agency charged with administering the CWA, EPA's role here is similar
to its baseline setting function in other aspects of the Act, to ensure
that there are sufficient authorities and limitations in place for
States and Tribes to effectively implement CWA programs within the
scope that Congress established. The final rule provides, for the first
time, a consistent framework to govern the implementation of CWA
section 401 that complies with the 1972 CWA amendments.
c. Administrative Procedure Act
    Some commenters asserted that the proposed rule is arbitrary and
capricious and an abuse of discretion. Some commenters cited Motor
Vehicle Mfrs. Ass'n of U.S., Inc. v. State Farm Mut. Auto., 463 U.S. 29
(1983), and argued that the EPA ``relied on factors which Congress has
not intended it to consider, entirely failed to consider an

important aspect of the problem, offered an explanation for its
decision that runs counter to the evidence before the agency or is so
implausible that it could not be ascribed to a difference in view or
the product of agency expertise.'' Id. at 43. One commenter asserted
that the EPA was arbitrary and capricious because the proposed rule
lacks analysis of water quality impacts and fails to consider whether
the proposed rule, if adopted, will ensure that the CWA's overarching
goal to protect water quality is met. This commenter further asserted
that when combined with the EPA's recent action to significantly narrow
the definition of ``waters of the United States,'' the effect of the
proposed rule could be to leave a regulatory gap, especially in cases
where federal law preempts State water quality regulations. Commenters
also argued, citing State Farm, 463 U.S. at 43, that the EPA failed to
``examine the relevant data and articulate a satisfactory explanation
for its action including a rational connection between the facts found
and the choice made.'' These commenters also cited Nat'l Cotton Council
of Am. v. EPA, 553 F.3d 927, 939 (6th Cir. 2009), and asserted that,
when the EPA adopts CWA regulations, it cannot ``ignore the directive
given to it by Congress . . . which is to protect water quality.'' One
commenter argued that the Agency elevated industrial interests over
State section 401 authority and therefore considered factors not
allowed by Congress in violation of the APA, citing Nat'l Lifeline
Ass'n v. FCC, 915 F.3d 19 (D.C. Cir. 2019) (quoting Motor Vehicle Mfrs.
Ass'n v. State Farm Mut. Auto Ins. Co., 463 U.S. 29, 43 (1983)).
    The final rule is neither arbitrary nor capricious nor an abuse of
the EPA's discretion. In crafting the final rule, the Agency started
with the statutory language of the CWA; where the plain language of the
Act was unclear or otherwise ambiguous, the EPA considered the
structure and purposes of the Act, relevant legal precedent, and
legislative history. The EPA also carefully considered the widely
varying and competing comments received during the pre-proposal
outreach, including Tribal and State engagement, and more than 125,000
public comments filed in the public docket, which are described
throughout this final rule preamble. These are factors that Congress
intended the Agency to consider. 5 U.S.C. 553(b) and (c). The Agency
carefully examined the statutory language and the legislative history
when determining the scope of certification and the appropriate role of
federal licensing and permitting agencies. The final rule promotes the
overarching goals of the CWA to prevent, reduce, and eliminate
pollution in the nation's waters and to regulate discharges into waters
of the United States, while preserving States' major role in
implementing the CWA. The Agency has examined relevant and available
data and articulated a robust basis for the rulemaking in the proposed
and final rule preambles. See the Economic Analysis and the Supporting
Statement for the Information Collection Request for the Clean Water
Act Section 401 Certification Rule for further discussion of available
data.
    Some commenters asserted the proposed rule is arbitrary and
capricious because it is a reversal of existing policy and that the
Agency did not provide adequate support for the policy reversal. Some
commenters argued that when an agency undertakes a new interpretation,
it needs a factual record on which to make such a change. These
commenters asserted that no record exists in the proposed rule and that
no recognition of prior State and EPA practice is evident. One
commenter argued that the EPA failed to provide a valid, reasoned basis
for departing from decades of agency practice. Some commenters also
asserted that the Agency did not demonstrate that the existing
regulations are inadequate or explain how the proposed rule will
provide increased predictability in comparison, noting that litigation
over section 401 denials falls short of a reasoned explanation. These
commenters argued that the proposed rule is just as likely to create
more confusion, unpredictability, and delay given the sweeping changes
that the proposed rule seeks to implement. Some commenters asserted
that the EPA was required to and has failed to conduct a careful
analysis of past certification reviews to demonstrate the need for the
proposed rule. Some commenters argued that the proposed rule does not
consider and analyze alternatives, as these commenters assert the
Agency is required to do, particularly when it proposes to reverse its
policy, citing State Farm, 463 U.S. at 46-48; Ctr. For Science in the
Pub. Interest v. Dep't of Treasury, 797 F.2d 995, 999 (D.C. Cir. 1986).
    The Agency disagrees with these commenters and concludes that its
justification in this rulemaking is more than adequate. The Agency's
final rule includes for the first time a well-defined scope for State
and Tribal review and actions under section 401. As articulated
throughout the proposal and this final rule preamble, the 1971
certification regulations were promulgated to implement section 21(b)
of the 1970 FWPCA, not section 401 of the 1972 CWA amendments. See
section II.F.3 of this notice. The 1972 amendments made two major
changes affecting the scope of the certification requirement: It
changed ``activity'' to ``discharge'' in section 401(a) and added
section 401(d), which describes effluent limitations, other
limitations, and monitoring requirements that may be included in a
certification. These important statutory elements were not present or
contemplated in the 1971 certification regulations, which the EPA is
updating with this final rule. It is entirely appropriate, and
necessary, for the EPA to conform to the 1972 CWA amendments when
updating its almost 50-year-old certification regulations. As noted
throughout the proposal preamble and the Economic Analysis, the EPA
acknowledges that many certifications reflect an appropriately limited
interpretation of the purpose and scope of section 401 and are issued
without controversy. Although a few high profile certification denials
are part of the factual and administrative record for this rulemaking,
and EPA has considered these facts during the rulemaking process, the
EPA has not relied on these facts as the sole or primary basis for this
rulemaking. The Agency's longstanding failure to update its regulations
created the confusion and regulatory uncertainty that were ultimately
the cause of those controversial section 401 certification actions and
the resulting litigation. To illustrate the type of uncertainty this
rule is attempting to resolve, recent court cases indicate that some
project proponents, certifying authorities and federal agencies have
different ideas about when the time for review of a certification
begins and--once begun--whether the review period can be tolled or
extend beyond one year. See Hoopa Valley Tribe v. FERC, 913 F.3d 1099
(D.C. Cir. 2019); New York State Dep't of Envtl. Conservation v. FERC,
884 F.3d 450 (2d Cir. 2018); Constitution Pipeline Co., LLC v. New York
State Dep't of Envtl. Conservation, 868 F.3d 87 (2d Cir. 2017).
Questions have also arisen regarding the role of the federal agency in
determining whether a waiver has occurred. Millennium Pipeline Co. v.
Seggos, 860 F. 3d 696 (D.C. Cir. 2017). Recent litigation also raises
the issue of a certifying authority's ability to deny certification for
other than water quality-related reasons. See Lighthouse Resources,
Inc. v. Inslee, No. 3:18-cv-5005 (W.D. Wash. filed Jan. 8, 2018).

    This rule updates the EPA's regulations to be consistent with the
language of section 401 as enacted in 1972. The final rule, while
focused on the relevant statutory provisions and case law interpreting
those provisions, is informed by the Agency's expertise developed over
nearly 50 years of implementing the CWA and policy considerations where
necessary to address certain ambiguities in the statutory text. For the
first time, this final rule aligns the EPA's regulations with the 1972
amendments and provides clarity to certifying authorities, federal
licensing and permitting agencies, project proponents, and the general
public.
    Other commenters asserted that the proposed rule is carrying out
the direction given by the Executive Order to stop States from
``hindering the development of energy infrastructure'' and asserted
that administrative action with such a predestined result should not be
afforded the level of deference typically afforded. Certain commenters
also cited Watt v. Alaska, 451 U.S. 259, 273 (1981), and General
Electric Co. v. Gilbert, 429 U.S. 125, 143 (1976), to argue that the
EPA is overturning fifty years of practice under the CWA in violation
of the clear language of 33 U.S.C. 1251(b), 33 U.S.C. 1341, and 33
U.S.C. 1370; and asserted that the EPA is entitled to less deference
when overturning past practice.
    The Agency disagrees that this rulemaking result was predetermined
by the Executive Order. As discussed in this final rule preamble, the
Executive Order does not specify details about what the regulation must
say, deferring to the Agency and its technical expertise, as informed
by public input, to develop a regulation consistent with the CWA. The
EPA issued a proposed rule, received public comment on that rule, made
changes in this final rule in response to comments and to increase
clarity and regulatory certainty for the section 401 certification
process, and explained the basis for these changes. None of that was
predetermined. The EPA further disagrees with commenters' assertions
that either the proposed rule or this final rule violates the CWA. As
described throughout this notice, the EPA for the first time conducted
a holistic analysis of the text, structure, and history of CWA section
401. The final rule is based on this holistic analysis and is
consistent with the language and congressional intent of section 401
and is informed by important policy considerations and the Agency's
expertise. Commenter's reliance on Watt v. Alaska, 451 U.S. 259 273,
(1981), and General Electric Co. v. Gilbert, 429 U.S. 125, 143 (1976),
is misplaced because both decisions pre-date Chevron and Brand X. As
described in section II.F.5 above, EPA has undertaken this rulemaking
in accordance with key principles of administrative law, respecting
unambiguous terms of the CWA and interpreting ambiguous language in
section 401 consistent with congressional intent. The EPA's approach
and rationale are set out in detail in the proposal and this final rule
preamble and are supported by applicable Supreme Court precedent.
d. Rulemaking Authority
    Several commenters cited A.L.A. Schechter Poultry Corp. v. United
States, 295 U.S. 495, 537-38 (1935), and argued that the proposed rule
is unconstitutional because it reflects the executive branch
legislating absent congressional delegation to do so. One commenter
asserted that federal executive agencies have no inherent authority to
make law and are subject to the legislative powers of the Congress.
This commenter cited Louisiana Pub. Serv. Comm'n v. FCC, 476 U.S. 355,
374 (1986), and argued that agency authority is limited to the
authority granted by Congress, and that the EPA cannot add conditions
outside the scope of the CWA for which Congress provided. Other
commenters asserted that by seeking to limit how States exercise their
authority under section 401, the proposed rule would exceed the
Agency's statutory authority ``to prescribe such regulations as are
necessary to carry out [the EPA Administrator's] functions under [the
Clean Water Act]'' (33 U.S.C. 1361(a)) and would instead intrude upon
the ``responsibilities and rights'' Congress expressly reserved to the
States. See 33 U.S.C. 1251(b). Other commenters agreed with the
proposal, stating that the EPA is tasked with promulgating rules for
the implementation of the CWA, including one commenter citing Alabama
Rivers Alliance v. FERC, 325 F.3d 290, 296-97 (2003).
    The EPA agrees that the section 401 rulemaking must be consistent
with the CWA and the EPA's authority under the Act, but disagrees with
commenters who asserted that the proposal or this final rule exceeded
that authority. Section 501 of the CWA gives the Administrator the
authority to adopt rules ``as are necessary to carry out his functions
under this chapter.'' 33 U.S.C. 1361(a). Section 101(d) of the CWA
expressly provides that the Administrator shall administer the CWA. 33
U.S.C. 1251(d). Section 401 of the CWA includes responsibilities for
the Administrator to issue certifications when a State or interstate
agency has no authority to issue a certification under section
401(a)(1), to ensure the protection of other States' waters under
section 401(a)(2), and to provide technical assistance under section
401(b). Section 304(h) of the CWA also specifically directs the EPA to
``promulgate guidelines establishing test procedures for the analysis
of pollutants that shall include the factors which must be provided in
any certification pursuant to section 401 of this Act.'' 33 U.S.C.
1314(h) (setting April 1973 deadline for doing so). The EPA is doing so
with this final rule.
    To carry out its functions under section 401, the EPA must adopt
rules that ensure transparency and accountability for actions taken
under section 401. This includes defining the scope of section 401 and
adopting appropriate procedures to implement the timing, public notice
and other requirements in section 401. Upon examination of the language
of section 401, the relevant case law and legislative history, the
Agency recognizes that section 401 contains some ambiguities and lacks
clarity in some sections. The Administrator's role under section
101(d), as the person charged with administering the CWA, includes
adopting reasonable interpretations of the statute to resolve
ambiguities and provide clarity. For example, because CWA section
304(h) requires the Administrator to develop guidelines that ``shall
include the factors that must be provided'' in any CWA section 401
certification, the EPA appropriately interprets that provision as
authorizing the Administrator to identify ``factors'' that may not be
included in a certification. The final rule presents a reasonable
interpretation of the scope of section 401, which, given the
ambiguities in sections 401(a) and 401(d), is properly the subject of
Agency interpretation. The final rule also requires certification
conditions and denials to be within that scope and that certain
information be included in a certification or denial to support the
action. These substantive and procedural regulations are necessary for
the Administrator to act as a certifying authority, to administer
section 401 provisions related to neighboring jurisdictions, and to
provide technical assistance to other certifying authorities, federal
agencies, and project proponents.
    Other commenters objected to the proposed rule, asserting that it
would disrespect the separation of powers by not implementing the will
of Congress as expressed in the CWA. U.S. Const.

art. II, Sec.  3. As discussed throughout this notice, the proposed
rule was consistent with statutory language of the CWA and
congressional intent, and this final rule appropriately implements the
will of Congress as expressed in the CWA.
    One commenter questioned the EPA's claim that it has the power to
alter ``unwise'' judicial decisions. A few commenters stated that
Chevron deference does not give a federal agency the power to rewrite
federal law, and they asserted, citing INS v. Cardozo-Fonseca, 480 U.S.
421 (1987); Adams Fruit Co. v. Barrett, 494 U.S. 638, 649-650 (1990);
Encino Motorcars, LLC. v. Navarro, 136 S. Ct. 2117 (2016); and Kisor v.
Wilkie, 139 S. Ct. 2400, 2417 (2019), that the proposed rule falls
outside the scope of Chevron deference. A few commenters argued that
the proposal's ``holistic'' review inappropriately found ambiguity in
the statutory language to justify drastic changes to the federal-State
relationship that section 401 established. These commenters argued that
instances where federal authority is encroaching on State authority
warrant heightened concern, citing SWANCC, 531 U.S. 159, 173 (2001),
and asserted that any changes must be based on a clear statement from
Congress.
    Other commenters stated that the divergent language of section
401(a) and section 401(d) creates ambiguity that needs to be resolved.
These commenters argued that the EPA's proposed interpretation is
reasonable and necessary to fill that statutory gap. One commenter
stated that the EPA correctly recognized that the Court's reliance on
Chevron deference in PUD No. 1 was entirely misplaced, as the Court did
not begin by first identifying an ambiguity in the statute, and the
Court ignored the fact that the EPA's own regulations at the time spoke
only in terms of ``discharges.'' A number of commenters agreed with the
EPA's proposal to address the ambiguities in the CWA statutory language
and the inconsistent application of the current regulations that impact
project applicants and other States' sovereignty. These commenters
agreed that the proposed rule would promote regulatory certainty, help
streamline the federal licensing and permitting process for critical
infrastructure development, enhance the ability of project proponents
to plan for construction, and facilitate early and constructive
engagement between permittees, States or authorized Tribes, and federal
agencies to ensure that proposed projects will be protective of local
water quality.
    As discussed in section II.F.5 of this notice, Chevron supplies the
appropriate framework for judicial review of statutory interpretation.
If the language of a congressional statute is clear, that unambiguous
meaning controls. If, however, the congressional text is ambiguous, a
reviewing court will defer to the implementing Agency's permissible
interpretation. Where, as in CWA section 401(a), Congress used
unambiguous terms like ``which shall not exceed one year'' and ``after
the receipt of such request,'' it is reasonable, indeed necessary, for
the Agency to apply the plain meaning of those terms when drafting its
implementing regulations. Where terms are ambiguous, such as ``other
appropriate requirement of State law'' in CWA section 401(d), the EPA
is authorized to fill the congressional gap and supply a reasonable
interpretation. Brand X supports the EPA's authority to interpret
ambiguous terms in section 401 and its ability to make reasonable
regulatory choices. That case recognizes that an Agency's statutory
interpretation is precluded only when, in a prior decision, a court
concluded that its contrary interpretation was compelled by the plain
language of the relevant text. Brand X, 545 U.S. at 982 (``[A] court's
prior judicial construction of a statute trumps an agency construction
otherwise entitled to Chevron deference only if the prior court
decision holds that its construction follows from the unambiguous terms
of the statute and thus leaves no room for agency discretion.''). None
of the EPA interpretations upon which its final regulatory language is
based, including the Agency's decision that section 401(d) limitations
and requirements may be placed only on the ``discharge'' and not on the
``activity,'' are inconsistent with that principle.

G. Legal Construct for the Final Rule

    As the preceding discussion demonstrates, the most challenging
aspects of section 401 concern the scope of review and action on a
certification request. The Agency is finalizing a regulation that will
clarify these aspects and provide additional regulatory certainty for
States, Tribes, federal agencies, and project proponents on the timing
and procedural requirements of the CWA. This section summarizes some of
the core legal principles that inform this final rule, and section III
of this notice describes how the Agency is applying those legal
principles to support the final rule.
1. Scope of Certification
    The EPA has for the first time conducted a holistic analysis of the
text, structure, and history of CWA section 401. As a result of that
analysis, the EPA is establishing the scope of section 401 as
protecting the quality of waters of the United States from point source
discharges associated with federally licensed or permitted activities
by requiring compliance with water quality requirements, as defined in
this final rule.
    Since at least 1973, the EPA has issued memoranda and guidance
documents, and the Department of Justice has filed briefs in various
court cases on behalf of the EPA, addressing section 401. Only a
handful of these documents address the scope of section 401, and none
was the product of a holistic examination of the statute or its
legislative history. As a result, these documents included little or no
explanation for the Agency's interpretations. For example, in 1989, the
EPA issued a guidance document asserting that a section 401
certification could broadly address ``all of the potential effects of a
proposed activity on water quality--direct and indirect, short and long
term, upstream and downstream, construction and operation. . . .'' EPA,
Wetlands and 401 Certification 23 (April 1989). The guidance document's
only explanation for this assertion is a reference to section
401(a)(3), which provides that a certification for a construction
permit may also be used for an operating permit that requires
certification. The guidance document, which did not undergo notice and
comment procedures, does not provide any analysis to support its
assertion that a certification could address all potential impacts from
the ``proposed activity'' as opposed to the discharge. Several years
later, the United States filed an amicus brief in the Supreme Court on
behalf of the EPA in the PUD No. 1 case. The amicus brief asserted that
petitioners were ``mistaken'' in their contention that the State's
minimum flow condition is outside the scope of section 401 because the
condition would be valid ``if it is necessary to assure that discharges
resulting from the project will comply with applicable provisions of
the CWA or `any other appropriate requirement of State law.' '' See
Brief for the United States as Amicus Curiae Supporting Affirmance, PUD
No. 1 of Jefferson County v. Washington Dep't of Ecology, No. 92-1911
at 11-12 (Dec. 1993) (emphasis added). The brief went on to identify
``two distinct discharges'' that would result from the petitioner's
facility and that would violate the CWA. The amicus brief did not offer
an affirmative interpretation to harmonize the different language in
sections 401(a)

and 401(d) and instead relied on the plain language in section 401(a).
More than a decade later, the United States' Supreme Court amicus brief
in the S.D. Warren case adopted without explanation the Supreme Court's
analysis in PUD No. 1 that once section 401 is triggered by a
discharge, a certification can broadly cover impacts from the entire
activity. Finally, in 2010, the EPA issued its now-rescinded Interim
Handbook, which included a number of recommendations on scope, timing,
and other issues, none of which were supported with robust analysis or
interpretation of the Act. The Interim Handbook, which did not undergo
notice and comment procedures either, also did not reference the fact
that the 1971 certification regulations were not updated after the CWA
was enacted in 1972.
    This rulemaking is the first time that the EPA has undertaken a
holistic review of the text of section 401 in the larger context of the
structure and legislative history of the 1972 Act and earlier federal
water protection statutes, and the first time the Agency has subjected
its analysis to public notice and comment. The final rule is informed
by this holistic review and presents a framework that the EPA considers
to be most consistent with the text of the Act and congressional
intent. After considering and taking into account the comments
submitted on the proposed rule, the Agency has made some enhancements
in this final rule to appropriately capture the scope of authority for
granting, conditioning, denying, and waiving a section 401
certification. For further discussion and response to comments on the
scope of certification, see section III.E of this notice.
a. Water Quality
    The EPA concludes that the scope of a State's or Tribe's section
401 review or action is not unbounded and must be limited to
considerations of water quality. Clarifying the proper scope in this
manner aligns with the objective of the CWA to restore and maintain
water quality (see CWA section 101(a)) Moreover, there is no suggestion
in either the plain language or the structure of the statute that
Congress envisioned section 401 to authorize action beyond that which
is necessary to address water quality directly. Indeed, as described in
greater detail above, the 1972 amendments to the CWA resulted in the
enactment of a comprehensive scheme designed to prevent, reduce, and
eliminate pollution in the nation's waters generally, and to regulate
the discharge of pollutants into waters of the United States
specifically.
    In its recent decision in County of Maui, Hawaii v. Hawaii Wildlife
Fund, et al., No. 18-260, the Supreme Court reaffirmed that ``Congress'
purpose as reflected in the language of the Clean Water Act is to
`restore and maintain the . . . integrity of the Nation's waters,'
Sec.  101(a)'' (Op. at 2, emphasis added) and underscored the
importance of interpreting the statutory text ``in light of the
statute's language, structure, and purposes'' in a manner that avoids
the creation of ``a massive loophole in the permitting scheme that
Congress established'' that would ``allow[ ] easy evasion of the
statutory provision's basic purposes.'' (Op. at 12, 15 (April 23,
2020)). The EPA's interpretation of the scope of CWA section 401 as
limited to considerations of water quality is fully consistent with
these fundamental principles and respects the congressional scheme at
issue in County of Maui. As discussed below and throughout the
preamble, this is also true of the Agency's other textual
interpretations that inform the definitions and requirements of this
rule relating to, for example, ``discharge,'' ``a reasonable period of
time (which shall not exceed one year,'' ``water quality
requirements,'' and ``any other appropriate requirement of State law.''
    The EPA is aware that some certifying authorities may have
previously interpreted the scope of section 401 in a way that resulted
in the incorporation of non-water quality-related considerations into
their certification review process. For example, certifying authorities
have on occasion required in a certification condition the construction
of biking and hiking trails, requiring one-time and recurring payments
to State agencies for improvements or enhancements that are unrelated
to the proposed federally licensed or permitted project, and the
creation of public access for fishing along waters of the United
States. Certifying authorities have also attempted to address all
potential environmental impacts from the creation, manufacture, or
subsequent use of products generated by a proposed federally licensed
or permitted activity or project that may be identified in an
environmental impact statement or environmental assessment, prepared
pursuant to the NEPA or a State law equivalent. This includes, for
example, consideration of impacts associated with air emissions and
transportation effects.
    The Agency has concluded that interpreting the scope of section 401
to allow States and Tribes to regulate and consider effects of an
activity rather than a discharge would invoke the outer limits of power
that Congress delegated to the Agency under the CWA. The imposition of
conditions unrelated to water quality is not consistent with the scope
of the CWA generally or section 401. There is nothing in the text of
the statute or its legislative history that signals that Congress
intended to impose, using section 401, federal requirements on licensed
or permitted activities beyond those addressing water quality-related
impacts. Indeed, Congress knows how to craft statutes to require
consideration of multi-media effects (see, e.g., NEPA), and has enacted
specific statutes addressing impacts to air (Clean Air Act), wildlife
(Endangered Species Act), and cultural resources (National Historic
Preservation Act), by way of example.\23\ Subsequent congressional
action directly addressing a particular subject is relevant to
determining whether a previously adopted statute reaches that subject
matter. See FDA v. Brown & Williamson Tobacco Corp., 529 U.S. 120, 155
(2000) (determining that ``actions by Congress over the past 35 years''
that addressed tobacco directly, when ``taken together,'' ``preclude[d]
an interpretation'' that a previously adopted statute, the Food, Drug,
and Cosmetic Act, ``grant[ed] the FDA jurisdiction to regulate tobacco
products.'').
---------------------------------------------------------------------------

    \23\ See, e.g., 42 U.S.C. 4321 et seq. (NEPA); 42 U.S.C. 7401 et
seq. (Clean Air Act); 16 U.S.C. 1531 et seq. (Endangered Species
Act); and 16 U.S.C. 470 et seq. (National Historic Preservation
Act).
---------------------------------------------------------------------------

    If Congress had intended section 401 of the CWA to authorize
consideration or the imposition of certification conditions based on
air quality or transportation concerns, public access to waters, energy
policy, or other multi-media or non-water quality impacts, it would
have provided a clear statement to that effect. Neither the CWA nor
section 401 contains any such clear statement. In fact, Congress
specifically contemplated a broader policy direction in the 1972
amendments that would have authorized the EPA to address impacts to
land, air, and water through implementation of the CWA, but it was
rejected.\24\ The Agency has concluded

that inclusion of the phrase ``any other appropriate requirement of
State law'' in section 401(d) hardly provides clear direction from
Congress that section 401(d) could extend beyond water quality.
Therefore EPA concludes that section 401(d)--like section 401(a) and
the rest of the Act--is limited to considerations of ``water quality.''
\25\
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    \24\ As Congress drafted the 1972 CWA amendments, the House bill
(H.R. 11896) included section 101(g) within its ``Declaration of
Goals and Policy'' providing, ``(g) In the implementation of this
Act, agencies responsible therefor shall consider all potential
impacts relating to the water, land, and air to insure that other
significant environmental degradation and damage to the health and
welfare of man does not result.'' H.R. 11896, 92nd Cong. (1971)
(emphasis added). Section 101(g) of the House bill was
``eliminated'' at conference, and the Act was ultimately passed with
no federal policy, goal, or directive to address non-water quality
impacts through the CWA. S. Rep. 92-1236, at 100 (1972) (Conf.
Rep.).
    \25\ The Agency also concludes that the term ``applicant'' in
section 401(d) creates ambiguity in the statute. See section
II.G.1.b of this notice for discussion of the use of the term
``applicant'' in section 401(d).
---------------------------------------------------------------------------

    Pursuant to the plain language of section 401, when a State or
authorized Tribe (and in some cases, the EPA) issues a certification,
it has determined that the discharge into waters of the United States
from a proposed federally licensed or permitted activity will comply
with applicable effluent limitations for new and existing sources (CWA
sections 301, 302, and 306), water quality standards and implementation
plans (section 303), toxic pretreatment effluent standards (section
307), and--by way of its power to add conditions pursuant to section
401(d)--other ``appropriate requirements'' of State or Tribal law. 33
U.S.C. 1341(a)(1), (d). The enumerated CWA provisions identify
requirements to ensure that discharges of pollutants do not degrade
water quality,\26\ and specifically referenced throughout section 401
is the requirement to ensure compliance with ``applicable effluent
limitations'' and ``water quality requirements,'' underscoring the
focused intent of this provision on the protection of water quality
from discharges.\27\ See 33 U.S.C. 1341(a), (b), (d). The legislative
history for the Act provides further support for the EPA's
interpretation, as it frequently notes that the focus of the section is
on assuring compliance with water quality requirements and water
quality standards and the elimination of any discharges of pollutants.
See, e.g., S. Rep. No. 92-414, at 69 (1971).
---------------------------------------------------------------------------

    \26\ For example, CWA section 306 defines the standard of
performance for new sources of discharges as ``a standard for the
control of the discharge of pollutants which reflects the greatest
degree of effluent reduction which the Administrator determines to
be achievable through application of best available demonstrated
control technology, processes, operating methods, or other
alternatives, including, where practicable, a standard permitting no
discharge of pollutants.'' 33 U.S.C. 1316(a)(1). Section 303 notes
that new or revised state water quality standards ``[s]hall be such
as to protect the public health or welfare, enhance the quality of
water and serve the purposes of this chapter.'' Id. at
1313(c)(2)(A).
    \27\ The term ``effluent limit'' is defined as, ``any
restriction established by a State or the Administrator on
quantities, rates, and concentrations of chemical, physical,
biological, and other constituents which are discharged from point
sources into navigable waters, the waters of the contiguous zone, or
the ocean, including schedules of compliance[,]'' 33 U.S.C.
1362(11); and the CWA requires that ``water quality standards''
developed by states and tribes ``consist of the designated uses of
the navigable waters involved and the water quality criteria for
such waters based upon such uses.'' Id. at 1313(c)(2)(A).
---------------------------------------------------------------------------

    The CWA does not define what is an ``appropriate requirement'' of
State law for purposes of adding conditions to a section 401
certification.\28\ In interpreting this term, the Agency acknowledges
the need to respect the clear policy direction from Congress to
recognize and preserve State authority over land and water resources
within their borders, see 33 U.S.C. 1251(b), and the Agency must avoid
interpretations of the CWA that infringe on traditional State land use
planning authority. See SWANCC, 531 U.S. at 172-73; Will, 491 U.S. at
65. One interpretation of this clause in section 401(d) could be that
it authorizes the denial of certification or the imposition of
conditions in a federal license or permit based on non-water quality-
related impacts if those requirements are based on any existing State
or Tribal law. Such an interpretation, however, is counterintuitive in
a statute aimed at protecting the ``chemical, physical, and biological
integrity of the nation's waters.'' For example, it is difficult to
imagine what guiding principle would help one determine whether to
import state labor law or professional licensing requirements into a
section 401 certification; such requirements could arguably be relevant
to a dam project, but mere relevance is not nearly sufficient to sweep
these types of laws within the ambit of an environmental statute aimed
at water quality. The CWA does not give EPA a clear basis to venture
into such regulatory arenas, which (in the absence of clearly expressed
congressional direction) are more appropriately reserved to the powers
of the States, ``powers with which Congress does not readily
interfere.'' Gregory, 501 U.S. at 461 (describing the ``plain statement
rule'').
---------------------------------------------------------------------------

    \28\ The EPA notes that during congressional hearings on the
1972 amendments, the House Committee was presented with testimony
that the term ``applicable water quality requirements'' should be
defined, but no definition was included in the enacted bill. See
section III.E.2.b for further discussion on this legislative
history.
---------------------------------------------------------------------------

    The Agency does not believe that Congress intended the phrase ``any
other appropriate requirement of State law'' to be read so broadly.
Instead, the ejusdem generis canon helps to inform the appropriate
interpretation of the statutory text. Under this principle, where
general words follow an enumeration of two or more things, they apply
only to things of the same general kind or class specifically
mentioned. See Wash. State Dept. of Social and Health Services v.
Keffeler, 537 U.S. 371, 383-85 (2003). Here, the general term
``appropriate requirement'' in section 401(d) follows an enumeration of
four specific sections of the CWA that are all focused on the
protection of water quality from point source discharges to waters of
the United States.\29\ Given the text, structure, purpose, and
legislative history of the CWA and section 401, and informed by
important policy considerations and the Agency's expertise, the EPA
interprets ``appropriate requirement'' for section 401 certification
purposes to include those provisions of State or Tribal law that
contain requirements for point source discharges into waters of the
United States, including provisions that are more stringent than
federal law. See S. Rep. No. 92-414, at 69 (1971) (``In addition, the
provision makes clear that any water quality requirements established
under State law, more stringent than those requirements established
under the Act, shall through certification become conditions on any
Federal license or permit.''). In this respect, the EPA agrees with the
logic of Justice Thomas's dissent in PUD No. 1, wherein he concludes
that ``the general reference to `appropriate' requirements of State law
is most reasonably construed to extend only to provisions that, like
other provisions in the list, impose discharge-related restrictions.''
PUD No. 1, 511 U.S. at 728 (Thomas, J., dissenting). The Agency's
interpretation gives meaning to Congress's decision to use the word
``appropriate'' in the phrase ``any other appropriate requirement of
State law set forth in such certification.''
---------------------------------------------------------------------------

    \29\ See Section II.G.1.c for further discussion on point source
discharges to waters of the United States in the context of section
401. Although section 401(a) mentions five sections of the CWA,
section 401(d) omits section 303. In PUD No. 1, the Court
interpreted section 303 to be included in section 401(d) by
reference to section 301. PUD No. 1, 511 U.S. at 712-13.
---------------------------------------------------------------------------

    Consistent with the proposal, the final rule limits the scope of
section 401 and the term ``appropriate requirements of State law'' to
those requirements directly related to water quality. As discussed in
greater detail in section III.E.2.b of this notice, the final rule
definition of ``water quality requirements'' has been modified from the
proposal, but does not stray from the core principle and focus of Title
IV of the CWA--to protect the quality of waters of the United States
from point source discharges.

b. Activity or Discharge
    Based on the text, structure, and legislative history of the CWA,
the EPA is affirming under this final rule that a certifying
authority's review and action under section 401 must be limited to
water quality impacts from the potential discharge associated with a
proposed federally licensed or permitted project. Section 401(a)
explicitly provides that the certifying authority, described as ``the
State in which the discharge originates or will originate,'' must
certify that ``any such discharge will comply with the applicable
provisions of sections 301, 302, 303, 306, and 307 of this Act''
(emphasis added). The plain language of section 401(a) therefore
directs authorities to certify that the discharge resulting from the
proposed federally licensed or permitted project will comply with the
CWA. Section 401(d) uses different language and requires the certifying
authority to ``set forth any effluent limitations and other
limitations, and monitoring requirements necessary to assure that any
applicant for a Federal license or permit will comply with any
applicable effluent limitations and other limitations, under section
301 or 302 of this title, standard of performance under section 306 of
this title, or prohibition, effluent standard, or pretreatment standard
under section 307 of this title, and with any other appropriate
requirement of State law set forth in such certification'' (emphasis
added).\30\ The use of the term ``applicant'' in section 401(d)--
instead of ``discharge'' as found in section 401(a)--creates ambiguity,
and has been interpreted as broadening the scope of section 401(a),
beyond consideration of water quality impacts from the ``discharge''
which triggers the certification requirement, to allow certification
conditions that address water quality impacts from any aspect of the
construction or operation of the activity as a whole. See PUD No. 1,
511 U.S. at 712.
---------------------------------------------------------------------------

    \30\ As a matter of practice, the Corps seeks State
certification for ``its own discharges of dredged or fill
material,'' ``[a]lthough the Corps does not process and issue
permits for its own activities.'' 33 CFR 336.1(a)(1).
---------------------------------------------------------------------------

    The ordinary meaning of the word ``applicant'' is ``[o]ne who
applies, as for a job or admission.'' See Webster's II, New Riverside
University Dictionary (1994). In section 401(d), this term is used to
describe the person or entity that applied for the federal license or
permit that requires a certification. The use of this term in section
401(d) is consistent with the text of the CWA, which uses the term
``applicant'' throughout to describe an individual or entity that has
applied for a grant, a permit, or some other authorization.\31\
Importantly, the term is also used in section 401(a) to identify the
person responsible for obtaining the certification: ``Any applicant for
a Federal license or permit to conduct any activity including, but not
limited to, the construction or operation of facilities, which may
result in any discharge into the navigable waters, shall provide the
licensing or permitting agency a certification from the State . . . .''
In the section 401 context, the term ``applicant'' also may include in
some circumstances the federal licensing or permitting agency, such as
where the federal agency is seeking certification for a general license
or permit.
---------------------------------------------------------------------------

    \31\ See, e.g., 33 U.S.C. 1311 (``An application for an
alternative requirement under this subsection shall not stay the
applicant's obligation to comply with the effluent limitation
guideline or categorical pretreatment standard which is the subject
of the application.''); id. at 1344 (``Not later than the fifteenth
day after the date an applicant submits all the information required
to complete an application for a permit under this subsection, the
Secretary shall publish the notice required by this subsection.'')
---------------------------------------------------------------------------

    Relying on the presence of the term ``applicant'' in section 401(d)
to interpret section 401(d) as allowing certification conditions that
are unrelated to a discharge would expand section 401 regulatory
authority beyond the scope of those sections of the Act enumerated in
section 401. Those enumerated CWA sections focus on regulating
discharges to waters of the United States. The Agency is not aware of
any other instance in which the term ``applicant'' (or permittee or
owner or operator) as used in the CWA has been interpreted to
significantly expand the jurisdictional scope or meaning of the
statute. The Agency therefore understands the term ``applicant'' in
section 401(d) as merely identifying the person or entity responsible
for obtaining and complying with the certification and any associated
conditions and not as expanding the regulatory scope of that section.
This interpretation of the term ``applicant,'' which appropriately ties
the term to the discharges that are the regulatory focus of section 401
as a whole and to the purposes of this section, is consistent with and
supported by the use in section 401(d) of the phrase ``applicant for a
Federal license or permit,' which refers back to the fuller phrase set
forth at the beginning of section 401(a): ``applicant for a Federal
license or permit to conduct any activity . . . which may result in any
discharge into the navigable waters.'' (Emphasis added.) This
interpretation also gives reasonable, and permissible, meaning to the
term ``appropriate'' in the phrase ``any other appropriate requirement
of State law set forth in such certification.'' The textual history and
legislative history of section 401, discussed below, provide additional
support for this interpretation.
    Section 401 was updated as part of the 1972 CWA amendments to
reflect the restructuring of the Act, as described in section II.F.1 of
this notice. Two important phrases were modified between the 1970 and
the 1972 versions of section 401 that help explain what Congress
intended with the 1972 amendments. First, the 1970 version provided
that an authority must certify ``that such activity . . . will not
violate water quality standards.'' Public Law 91-224 Sec.  21(b)(1)
(emphasis added). Significantly, Congress modified this language in
1972, requiring an authority to certify ``that any such discharge shall
comply with the applicable provisions of [the CWA].'' 33 U.S.C. 1341(a)
(emphasis added). On its face, this modification made the 1972 version
of section 401 consistent with the overall framework of the amended
statutory regime, which focuses on regulating discharges to attain
water quality standards and adds new federal regulatory programs to
achieve that purpose. 33 U.S.C. 1311, 1312, 1313, 1316, 1317, 1342 and
1344.
    Second, the 1972 version included section 401(d) for the first
time. This provision authorizes conditions to be imposed on a
certification ``to assure that any applicant for a Federal license or
permit will comply with any applicable effluent limitations and other
limitations, under section 301 or 302 of this Act, standard of
performance under section 306 of this Act, or prohibition, effluent
standard, or pretreatment standard under section 307 of this Act, and
with any other appropriate requirement of State law set forth in such
certification . . . .''Id. at 1341(d). This new section also requires
such conditions to be included in the federal license or permit. Id.
    Together, these amendments to the pre-1972 statute focus section
401 on discharges that may affect water quality, enumerate newly
created federal regulatory programs with which section 401 mandates
compliance, and require that water quality-related certification
conditions be included in federal licenses and permits and thereby
become federally enforceable. The legislative history describing these
changes supports a conclusion that the provisions were added
intentionally and with the purpose of making the new section 401
consistent with the new

framework of the Act. Indeed, the 1971 Senate Report provided that
section 401 was ``amended to assure consistency with the bill's changed
emphasis from water quality standards to effluent limitations based on
the elimination of any discharge of pollutants.'' S. Rep. No. 92-414,
at 69 (1971).
    An EPA attorney previously analyzed the modifications made to
section 401 between the 1970 and 1972 Acts. See Memorandum from
Catherine A. Winer, Attorney, EPA Office of General Counsel, Water
Division, to David K. Sabock, North Carolina Department of Natural
Resources (Nov. 12, 1985).\32\ In its analysis, the attorney
characterized the legislative history quoted above as ``not very
explicit,'' and characterized the new section 401 language as ``not
altogether clear.'' Id. Based on this analysis, the attorney found at
that time that ``the overall purpose of section 401 is clearly `to
assure that Federal licensing or permitting agencies cannot override
water quality requirements' '' and that ``section 401 may reasonably be
read as retaining its original [i.e., pre-1972] scope, that is,
allowing state certifications to address any water quality standard
violation resulting from an activity for which a certification is
required, whether or not the violation is directly caused by a
`discharge' in the narrow sense.'' Id. (citing S. Rep. No. 92-414, at
69 (1971)).
---------------------------------------------------------------------------

    \32\ Available at https://www.epa.gov/sites/production/files/2015-01/documents/standards-marinas-memo.pdf.
---------------------------------------------------------------------------

    The EPA has now performed a holistic analysis of the text and
structure of the CWA, the language of section 401, and the amendments
made between 1970 and 1972. Based on this review, the EPA now concludes
that the 1972 version of section 401 made specific changes to ensure
that discharges were controlled in compliance with the 1972 CWA
regulatory programs and appropriate requirements of State law. For the
reasons noted above in section II.F.1 of this notice, identifying and
regulating discharges, as opposed to managing ambient water quality,
promotes accountability and enforcement of the Act in a way that the
1970 and earlier versions did not. The EPA also observes that, had
Congress intended the 1972 amendments to retain the original scope
concerning ``activity,'' it could have easily crafted section 401(d) to
authorize certification conditions to assure that ``the activity''
would comply with the specified CWA provisions, but it did not.
Instead, Congress' use of the term ``discharge'' in section 401(a)
frames the scope of the certification requirement under the Act. As a
result, the Agency now considers a more natural and more reasonable
interpretation of the 1972 amendments to be that Congress rejected the
idea that the scope of a certifying authority's review or its
conditions should be defined by the term ``activity.'' Congress
specifically did not carry forward the term ``activity'' in the
operative phrase in section 401(a) and did not incorporate it into the
new provision authorizing certification conditions in section 401(d).
Under basic canons of statutory construction, the EPA begins with the
presumption that Congress chose its words intentionally. See, e.g.,
Stone v. INS, 514 U.S. 386, 397 (1995) (``When Congress acts to amend a
statute, we presume it intends its amendment to have real and
substantial effect.''). This is also consistent with the dissent in PUD
No. 1, wherein Justice Thomas concluded that ``[i]t is reasonable to
infer that the conditions a State is permitted to impose on
certification must relate to the very purpose the certification process
is designed to serve. Thus, while Sec.  401(d) permits a State to place
conditions on a certification to ensure compliance of the
`applicant'[,] those conditions must still be related to discharges.''
PUD No. 1, 511 U.S. at 726-27 (Thomas, J., dissenting). The EPA has
concluded that this interpretation is reasonable and the most
appropriate reading of the statute and related legal authorities.
    As described in detail in section II.F.4.a.i of this notice, the
Supreme Court in PUD No. 1 considered the scope of a State's authority
to condition a section 401 certification. In response to petitioners'
argument in that case that certification conditions may only be limited
to the ``discharge'' referenced in section 401(a), the Court noted that
``[t]he text refers to the compliance of the applicant, not the
discharge.'' Id. at 712. Without further analysis of the ambiguity
created by the use of the term ``applicant'' in section 401(d), the
Court concluded that ``Sec.  401(d) is most reasonably read as
authorizing additional conditions and limitations on the activity as a
whole once the threshold condition, the existence of a discharge, is
satisfied.'' Id. at 712. The Court did not grapple with the range of
actions that its interpretation may require of the applicant, or
whether the entire range would or should be within the scope of section
401. The Court did not evaluate or find support for its interpretation
in the legislative history of the 1972 amendments to the CWA, nor did
the Court find that Congress had established an intent that the term
``applicant'' in section 401(d) should mean ``activity.'' Although some
have argued that the Court's conclusion is based on a plain language
interpretation of section 401(d), for the reasons explained below, the
EPA disagrees. The EPA concludes that the use of the term ``discharge''
in section 401(a) and ``applicant'' in section 401(d) creates
ambiguity, that the plain text of 401(d) also is ambiguous, and that
neither the Court's analysis nor its holding in PUD No. 1 foreclose
alternative interpretations.
    In its discussion of the CWA, the Supreme Court in PUD No. 1 did
not analyze section 401 at ``Chevron step one'' or rely on ``the
unambiguous terms'' of the CWA to support its reading of section 401.
See Brand X, 545 U.S. at 982. Instead, the Court ``reasonably read''
section 401(d) ``as authorizing additional conditions and limitations
on the activity as a whole once the threshold condition, the existence
of a discharge, is satisfied.'' PUD No. 1, 511 U.S. at 712 (emphasis
added). To support what it considered to be a reasonable reading of
section 401(d), the Court looked at the EPA's 1971 certification
regulations at 40 CFR 121.2(a)(3) and related guidance available at
that time, PUD No. 1, 511 U.S. at 712, but the Court did not have
before it the EPA's interpretation of how sections 401(a) and 401(d)
could be harmonized. In fact, the Court either was not aware of or did
not mention that the EPA's 1971 certification regulations in place at
that time predated the 1972 CWA amendments and therefore contained
outdated terminology implementing what was functionally a different
statute. As described above, the EPA's 1971 certification regulations
were consistent with the text of the pre-1972 CWA, and they required a
State to certify that the ``activity'' will comply with the Act. The
1972 CWA amendments changed this language to require a State to certify
that the ``discharge'' will comply with the Act.
    Based in part on what the EPA now recognizes was infirm footing,
the Court found that ``EPA's conclusion that activities--not merely
discharges--must comply with state water quality standards is a
reasonable interpretation of Sec.  401 and is entitled to deference.''
Id. (emphasis added). As amicus curiae in the Supreme Court, the United
States did not seek Chevron ``deference for the EPA's regulation in
[the PUD No. 1 case]'' or for the EPA's interpretation of section 401.
Id. at 729 (Thomas, J., dissenting). In fact, the United States' amicus
brief for the Court did not analyze or interpret the different

language in sections 401(a) and 401(d) and instead asserted that it was
unnecessary to harmonize the provisions to resolve the dispute. See
Brief for the United States as Amicus Curiae Supporting Affirmance, PUD
No. 1 of Jefferson County v. Washington Dep't of Ecology, No. 92-1911
at 12 n. 2 (Dec. 1993). The amicus brief asked the Court to analyze the
two undisputed discharges from the proposed federally licensed project
and to determine whether they would cause violations of the State's
water quality standards. Id. at 11-16.
    Given the circumstances of the PUD No. 1 litigation, and the fact
that the Supreme Court did not analyze section 401 under Chevron step 1
or rely on unambiguous terms in the CWA to support its interpretation
of the statute, PUD No. 1 does not foreclose the Agency's
interpretation of section 401 in this final rule. See Brand X, 545 U.S.
at 982-83. The Supreme Court's ``choice of one reasonable reading'' of
section 401 does not prevent the EPA ``from later adopting a different
reasonable interpretation.'' \33\ Eurodif S.A., 555 U.S. at 315. An
agency may engage in ``a formal adjudication or notice-and-comment
rulemaking'' to articulate its interpretation of an ambiguous statute.
Christensen v. Harris County, 529 U.S. 576, 587 (2000). When it does,
courts apply ``Chevron-style'' deference to the agency's
interpretation. Id. That is exactly what the EPA is doing in this final
rule. The EPA has for the first time, holistically interpreted the text
of sections 401(a) and 401(d) to support this update to the Agency's
1971 certification regulations while ensuring consistency with the
plain language of the 1972 CWA.
---------------------------------------------------------------------------

    \33\ The EPA is not modifying the Agency's longstanding
interpretation of the Act that was confirmed by the Court in PUD No.
1 that ``a water quality standard must `consist of the designated
uses of the navigable waters involved and the water quality criteria
for such waters based upon such uses' '' and that ``a project that
does not comply with a designated use of the water does not comply
with the applicable water quality standards.'' 511 U.S. at 714-15
(emphasis in original; quoting 33 U.S.C. 1313(c)(2)(A)).
---------------------------------------------------------------------------

c. Discharges From Point Sources to Waters of the United States
    Based on the text, structure, and purpose of the Act, the history
of the 1972 CWA amendments, relevant legislative history, and
supporting case law, and informed by important policy considerations
and the Agency's expertise, the EPA has concluded that a certifying
authority's review and action under section 401 is limited to water
quality impacts to waters of the United States resulting from a
potential point source discharge from a proposed federally licensed or
permitted project. The text of section 401(a) clearly specifies that
certification is required for any federal license or permit to
``conduct any activity . . . which may result in any discharge into the
navigable waters'' (emphasis added). Prior interpretations extending
section 401 applicability beyond such waters conflict with and would
render meaningless the plain language of the statute. And although the
statute does not define with specificity the meaning of the unqualified
term discharge, interpreting section 401 to cover all discharges
without qualification would undercut the bedrock structure of the CWA
regulatory programs, which are focused on addressing point source
discharges to waters of the United States. CWA section 502(14) defines
``point source'' as ``any discernible, confined and discrete
conveyance, including but not limited to any pipe, ditch, channel,
tunnel, conduit, well, discrete fissure, container, rolling stock,
concentrated animal feeding operation, or vessel or other floating
craft, from which pollutants are or may be discharged.'' \34\
---------------------------------------------------------------------------

    \34\ In the section 404 context, point sources include
bulldozers, mechanized land clearing equipment, dredging equipment,
and the like. See, e.g., Avoyelles Sportsmen's League, Inc. v.
Marsh, 715 F.2d 897, 922 (5th Cir. 1983).
---------------------------------------------------------------------------

    As described in section II.F.1 of this notice, the CWA is
structured such that the federal government provides assistance,
technical support, and grant money to assist States in managing all of
the nation's waters. By contrast, the federal regulatory provisions,
including CWA sections 402 and 404, apply only to point source
discharges to waters of the United States. 33 U.S.C. 1362(7). Section
401 is the first section of Title IV of the CWA, titled Permits and
Licenses, and it requires water quality-related certification
conditions to be legally binding and federally enforceable conditions
of federal licenses and permits. Id. at 1341(d). Similar to the section
402 and 404 permit programs, section 401 is a core regulatory provision
of the CWA. Accordingly, the scope of its application is most
appropriately interpreted, consistent with the other federal regulatory
programs, as addressing point source discharges into waters of the
United States.
    The EPA is not aware of any court decisions that have directly
addressed the scope of waters covered by section 401; however, the
plain text of section 401 is clear and EPA's interpretation is
supported by legislative history (see section II.G.1.b of this notice).
Additionally, public commenters noted that many state Attorneys General
submitted comments on the Agency's rulemaking to define ``waters of the
United States'' asserting that modifying that definition would modify
the scope of state review under section 401, further supporting the
EPA's interpretation that section 401 is limited to waters of the
United States.
    In Oregon Natural Desert Association v. Dombeck, the Ninth Circuit
relied on the text and structure of section 401 to interpret the
meaning of ``discharge'' in section 401. 172 F.3d 1092 (9th Cir. 1998).
In that case, a citizen's organization challenged a decision by the
U.S. Forest Service to issue a permit to graze cattle on federal lands
without first obtaining a section 401 certification from the State of
Oregon. The government argued that a certification was not needed
because the ``unqualified'' term ``discharge''--as used in CWA section
401--is ``limited to point sources but includes both polluting and
nonpolluting releases.'' Id. at 1096. Finding that the 1972 amendments
to the CWA ``overhauled the regulation of water quality,'' the court
said that ``[d]irect federal regulation [under the CWA] now focuses on
reducing the level of effluent that flows from point sources.'' Id. The
court stated that the word ``discharge'' as used consistently in the
CWA refers to the release of effluent from a point source. Id. at 1098.
The court found that cattle--even if they wade in a stream--are not
point sources. Id. at 1098-99. Accordingly, the court held that
certification under section 401 was not required. Id. at 1099.
    The EPA previously suggested that the scope of section 401 may
extend to nonpoint discharges to non-federal waters \35\ once the
requirement for the section 401 certification is triggered.
Specifically, in the EPA's now-withdrawn Interim Handbook, the Agency
included the following paragraphs,
---------------------------------------------------------------------------

    \35\ Non-federal waters refer to those waters that are not
waters of the United States.

    The scope of waters of the U.S. protected under the CWA includes
traditionally navigable waters and also extends to include
territorial seas, tributaries to navigable waters, adjacent
wetlands, and other waters. Since Sec.  401 certification only
applies where there may be a discharge into waters of the U.S., how
states or tribes designate their own waters does not determine
whether Sec.  401 certification is required. Note, however, that
once Sec.  401 has been triggered due to a potential discharge into
a water of the U.S., additional waters may become a consideration in
the certification decision if it [sic] is an aquatic resource
addressed by

``other appropriate provisions of state [or tribal] law.''
* * * * *
    Section 401 applies to any federal permit or license for an
activity that may discharge into a water of the U.S. The Ninth
Circuit Court of Appeals ruled that the discharge must be from a
point source, and agencies in other jurisdictions have generally
adopted the requirement. Once these thresholds are met, the scope of
analysis and potential conditions can be quite broad. As the U.S.
Supreme Court has held, once Sec.  401 is triggered, the certifying
state or tribe may consider and impose conditions on the project
activity in general, and not merely on the discharge, if necessary
to assure compliance with the CWA and with any other appropriate
requirement of state or tribal law.

    Interim Handbook, 5, 18 (citations omitted). To support the first
referenced paragraph on the scope of waters, the Interim Handbook cited
section 401(d), presumably referring to the use of the term
``applicant'' rather than ``discharge'' used in section 401(a).\36\ To
support the second paragraph on the scope of discharges, the Interim
Handbook cited the PUD No. 1 and S.D. Warren Supreme Court decisions.
It appears that both paragraphs from the Agency's Interim Handbook
relied on the PUD No. 1 Court's interpretation of the ambiguity created
by the different language in sections 401(a) and 401(d).\37\
---------------------------------------------------------------------------

    \36\ Interim Handbook, at 5 n. 23. Tellingly, footnote 23 of the
Interim Handbook also states, ``Note that the Corps may consider a
401 certification as administratively denied where the certification
contains conditions that require the Corps to take an action outside
its statutory authority or are otherwise unacceptable. See, e.g.,
RGL 92-04, `Section 401 Water Quality Certification and Coastal Zone
Management Act Conditions for Nationwide Permits.''
    \37\ The S.D. Warren decision did not analyze or adopt the PUD
No. 1 Court's analysis of sections 401(a) and 401(d).
---------------------------------------------------------------------------

    For many of the same reasons why the Agency is not interpreting the
use of the word ``applicant'' in section 401(d) as broadening the scope
of certification beyond the discharge itself, the Agency is also
declining to interpret section 401(d) as broadening the scope of waters
and the types of discharges to which the CWA federal regulatory
programs apply. As an initial matter, the Agency agrees with the Ninth
Circuit's analysis and holding in Dombeck that section 401
certification is not required for nonpoint source discharges. Oregon
Natural Desert Association v. Dombeck, 172 F.3d 1092, 1098-99 (9th Cir.
1998). Were the Agency to interpret the use in section 401(d) of the
term ``applicant'' instead of the term ``discharge'' as authorizing the
federal government to implement and enforce CWA conditions on, or that
affect, non-federal waters, that single word (``applicant'') would
effectively broaden the scope of the federal regulatory programs
enacted by the 1972 CWA amendments beyond the limits that Congress
intended. Such an interpretation could permit the application of the
CWA's regulatory programs, including section 401 certification
conditions that are enforced by federal agencies, to land and water
resources more appropriately subject to traditional State land use
planning authority where not otherwise preempted by federal law. See,
e.g., SWANCC, 531 U.S. at 172-73.
    As described in section II.F.4.a.i of this notice and pursuant to
its authority to reasonably interpret ambiguous statutes to fill gaps
left by Congress, the EPA is interpreting the language in sections
401(a) and (d) differently than the Supreme Court did in PUD No. 1. The
Court's prior interpretation, that once a ``discharge'' triggers the
certification requirement in section 401(a) the certification itself
may cover the entire ``activity,'' was not based on the plain
unambiguous text of the statute, but rather was based on the Court's
own interpretation of ambiguous text in light of the interpretation of
the statute set forth in the 1971 certification regulations (see
section II.F.4.a.i of this notice). The EPA's interpretation under this
final rule is also based on a reasonable interpretation of the text,
structure, and legislative history of section 401 and is informed by
important policy considerations and the Agency's expertise, and the
Agency's current rule is not foreclosed by the Court's prior
interpretation. See Brand X, 545 U.S. at 982.
    For the reasons above, the EPA is concluding that section 401 is a
regulatory provision that creates federally enforceable requirements,
and for this and other reasons, its application must be limited to
point source discharges into waters of the United States. This
interpretation is consistent with the text and structure of the CWA as
well as the principal purpose of this rulemaking, i.e., to ensure that
the EPA's regulations (including those defining a section 401
certification's scope) are consistent with the current CWA.\38\ For
further discussion on the Agency's interpretation and comments received
on discharges under section 401, see section III.A.2.a of this notice.
---------------------------------------------------------------------------

    \38\ Although the legislative history on section 401 sometimes
lacks clarity and can be internally inconsistent, the Agency's
interpretation is consistent with much of the legislative history
from the 1972 amendments. See, e.g., H.R. Rep. No. 92-911, at 124
(1972) (``It should be clearly noted that the certifications
required by section 401 are for activities which may result in any
discharge into navigable waters. It is not intended that State
certification is or will be required for discharges into the
contiguous zone or the oceans beyond the territorial seas.''); 118
Cong, Rec. 33,692, 33,698 (1972) (``[t]he Conferees agreed that a
State may attach to any Federally issued license or permit such
conditions as may be necessary to assure compliance with water
quality standards in that State.''); S. Rep. No. 92-411, at 69
(1971) (``This section is substantially 21(b) of existing law
amended to assure consistency with the bill's changed emphasis from
water quality standards to effluent limitations based on the
elimination of any discharge of pollutants.'' (parentheticals
omitted)); 117 Cong. Rec. 38,797, 38,855 (1971) (Mr Muskie:
``Sections 401 and 402 provide for controls over discharge.'')
---------------------------------------------------------------------------

2. Timeline for Section 401 Certification Analysis
    Based on the language of the CWA and consistent with the relevant
case law, the EPA is clarifying that a certifying authority must act on
a section 401 certification within a reasonable period of time, which
shall not exceed one year, and that there is no tolling provision to
stop the clock at any time.
    The text of section 401 expressly states that a certifying
authority must act on a section 401 certification request within a
reasonable period of time, which shall not exceed one year. 33 U.S.C.
1341(a)(1). Importantly, as the words ``shall not exceed'' suggest, the
CWA does not guarantee that a certifying authority may take a full year
to act on a section 401 certification request. The certifying authority
may be subject to a shorter period of time, provided it is reasonable.
See Hoopa Valley Tribe v. FERC, 913 F.3d 1099, 1104 (DC Cir. 2019)
(``Thus, while a full year is the absolute maximum, it does not
preclude a finding of waiver prior to the passage of a full year.
Indeed, the [EPA]--the agency charged with administering the CWA--
generally finds a state's waiver after only six months.'' (citing 40
CFR 121.16)). The CWA's legislative history indicates that inclusion of
a maximum period of time was to ``insure that sheer inactivity by the
[certifying authority] will not frustrate the Federal application.''
H.R. Rep. No. 92-911, at 122 (1972).
    The timeline for action on a section 401 certification must
conclude within a reasonable period of time (not to exceed one year)
after receipt of a certification request. Id.; 33 U.S.C. 1341(a)(1).
The CWA does not specify any legal requirements for what constitutes a
request or otherwise define the term. As discussed further in section
III.C, this final rule addresses that ambiguity to provide additional
clarity and regulatory certainty. Additionally,

the EPA has long recommended that a project proponent requiring a
federal license or permit subject to section 401 certification hold
early discussions with both the certifying authority and the federal
agency, to better understand the certification process and potential
data or information needs.
    The CWA does not contain provisions for tolling the timeline for
any reason, including to request or receive additional information from
the project proponent. If the certifying authority has not acted on a
request for certification within the reasonable time period, the
certification requirement will be waived and the federal agency may
proceed to issue the license or permit.
    The final rule provides for specific timeframes for certain
procedural requirements (e.g., pre-meeting filing requests, discussed
in final rule preamble section III.B; and public notice when EPA acts
as the certifying authority, discussed in final rule preamble section
III.H). Throughout this final rule, EPA intends that the term ``days''
refers to calendar days as opposed to business days. For further
discussion on the Agency's interpretation of the timeline for section
401 certification analysis and related comments, see section III.F of
this notice. This final rule is intended to provide greater clarity and
certainty and to address some of the delays and confusion associated
with the timing elements of the section 401 certification process.

III. Final Rule

    This final rule is intended to make the Agency's regulations
consistent with the current text of CWA section 401, increase
efficiencies, and clarify aspects of CWA section 401 that have been
unclear or subject to differing legal interpretations in the past. The
Agency is replacing the entirety of the 1971 certification regulations
at 40 CFR part 121 with this final rule. The following sections further
explain the Agency's rationale for the final rule, provide a detailed
explanation and analysis for the substantive changes that the Agency is
finalizing, and respond to significant public comments received on the
proposed rule.
    The EPA's 1971 certification regulations were issued when the
Agency was but a few months old and the CWA had not yet been amended to
include the material revisions to section 401.\39\ In modernizing 40
CFR part 121, this final rule recognizes and responds to significant
changes to the CWA that occurred after the 1971 regulations were
finalized, especially the 1972 and 1977 amendments to the CWA.
---------------------------------------------------------------------------

    \39\ See 36 FR 22487, Nov. 25, 1971, redesignated at 37 FR
21441, Oct. 11, 1972, further redesignated at 44 FR 32899, June 7,
1979; Reorganization Plan No. 3 of 1970 (creating the EPA), 84 Stat.
2086, effective Dec. 2, 1970.
---------------------------------------------------------------------------

    Updating the 1971 certification regulations to clarify
expectations, timelines, and deliverables also increases efficiencies.
Some aspects of the 1971 certification regulations have been
implemented differently by different authorities, likely because the
scope and timing of review were not clearly addressed in EPA's
regulations. While the EPA recognizes that States and Tribes have broad
authority to implement State and Tribal law to protect their water
quality, see 33 U.S.C. 1251(b), section 401 is a federal regulatory
program that contains limitations on when and how States and Tribes may
exercise this particular authority. This final rule modernizes and
clarifies the EPA's regulations and will help States, Tribes, federal
agencies, and project proponents know what is required and what to
expect during a section 401 certification process, thereby reducing
regulatory uncertainty. For further discussion on ways the final rule
will reduce regulatory uncertainty, see the Economic Analysis available
in the docket for this final rule.
    The EPA's 1971 certification regulations did not fully address the
public notice requirements called for under CWA section 401(a)(1). The
EPA is finalizing public notice requirements applicable to the EPA as
the certifying authority but is not extending these requirements to
other certifying authorities. The EPA encourages certifying authorities
to consider how their public notice requirements can be developed or
modified to ensure timely decision-making and to work with federal
licensing and permitting agencies to minimize conflicts between State
program administration and the federally established reasonable period
of time.
    Because the EPA has frequently received requests for information
regarding certifying authority requirements, the Agency solicited
comment on whether it would be appropriate or necessary to require
certifying authorities to submit their section 401 procedures and
regulations to the EPA for informational purposes. One commenter stated
that it would be useful for the EPA to compile procedures of certifying
authorities and make these publicly available in one location, while
another commenter stated that it was unnecessary and inappropriate for
the EPA to compile procedures of certifying authorities. Some
commenters stated that it is not necessary for certifying authorities
to submit their section 401 certification procedures and regulations to
the EPA. One commenter noted that their procedures are public
information available on the state website. Another commenter stated
that a regulation that requires submittal of section 401 procedures is
unnecessary and duplicative because the State already works with the
EPA on section 401 procedures.
    The EPA has considered these comments, and the final rule does not
include a requirement for certifying authorities to submit their
procedures to the EPA. However, to promote transparency and regulatory
certainty, the EPA strongly encourages certifying authorities to make
their certification regulations and any ``water quality requirements''
that may be considered during a certification process available online.
In the interest of transparency, clarity, and public accessibility, the
EPA may consider compiling certifying authorities' procedures and water
quality requirements on its website in the future.
    In addition to the substantive changes in the final rule described
below, the Agency made a number of revisions to streamline and clarify
the regulatory text, and to more closely align that text to the
language in section 401. These changes include revising the definitions
of ``Administrator'' and ``discharge''; replacing the language
``proposed discharge location'' in section 121.11(a) with ``facility or
activity'' for consistency with section 401; revising certain text in
sections 121.7(f), 121.12, and 121.16 for consistency with section 401;
and removing redundant language throughout the final rule.

A. When Section 401 Certification Is Required

1. What is the Agency finalizing?
    Under this final rule, the requirement for a section 401
certification is triggered based on the potential for any federally
licensed or permitted activity to result in a discharge from a point
source into waters of the United States. Consistent with section
401(a)(1), section 121.2 of the final rule provides that:
    Certification is required for any license or permit that authorizes
an activity that may result in a discharge.
    This provision is modified from the proposal to provide greater
clarity regarding when a certification is

required, but the Agency does not intend for this change to alter the
meaning of the provision from the proposal. This final rule preamble
also clarifies in section III.M that certification also is required
before a federal agency issues a general license or permit which may
result in a discharge. As discussed further below, in the final rule
the term ``discharge'' is defined to mean a point source discharge into
a water of the United States, and the term ``license or permit'' is
defined to mean a license or permit issued by a federal agency to
conduct any activity which may result in a discharge. The final rule
reflects that section 401 is triggered by the potential for a discharge
to occur, rather than an actual discharge.
2. Summary of Final Rule Rationale and Public Comment
    Section 121.2 of the final rule is consistent with the Agency's
longstanding interpretation and is not intended to alter the scope of
applicability established in the CWA.
a. ``Discharge''
    In section 401 and under the final rule, the presence of, or
potential for, a discharge is a key element of when a water quality
certification is required. Consistent with the text of the statute,
under the final rule section 401 is triggered by the potential for a
discharge to occur, rather than the presence of an actual discharge.
The final rule defines the term ``discharge'' consistent with the
proposal but replaces the term ``navigable waters'' in the proposed
definition with ``waters of the United States'' in the final
definition. This change is not intended to change the meaning of the
definition; rather, it provides clarity and consistency across other
CWA programs.
    Many commenters agreed that the requirement for a section 401
certification is triggered by the potential for a discharge from a
federally licensed or permitted activity. One commenter stated that the
EPA's reliance on an actual discharge would disregard the broad scope
of section 401, which is designed to consider all potential discharges
over the life of a federally licensed or permitted activity. One
commenter stated that the proposed definition of ``discharge'' does not
contemplate a potential discharge. The commenter asserted that such an
interpretation would conflict with the text of section 401 which states
that water quality certification applies to any ``federal license or
permit to conduct any activity . . . which may result in a discharge.''
    The EPA agrees with commenters that the language of the statute
triggers the section 401 certification requirement based on a potential
discharge.\40\ Section 401 is different from other parts of the Act
\41\ and provides certifying authorities with a broad opportunity to
review proposed federally licensed or permitted projects that may
result in a discharge into waters of the United States within their
borders. The Agency does not agree that the concept of ``potential''
must be incorporated into the rule text definition of ``discharge''
itself; the final rule provision at section 121.2 clearly states that a
401 certification is required for ``an activity which may result in a
discharge'' (emphasis added).
---------------------------------------------------------------------------

    \40\ A certification is required for ``a Federal license or
permit to conduct any activity . . . which may result in any
discharge into the navigable waters . . .'' 33 U.S.C. 1341(a)(1)
(emphasis added).
    \41\ See, e.g., National Pork Producers Council v. EPA, 635 F.3d
738, 751 (5th Cir. 2011) (holding that ``the EPA cannot impose a
duty to apply for a permit on a [concentrated animal feeding
operation] that `proposes to discharge' or any CAFO before there is
an actual discharge.''); Waterkeeper Alliance, Inc. v. EPA, 399 F.3d
486, 505 (2d Cir. 2005) (same).
---------------------------------------------------------------------------

    In the proposal, the EPA requested that certifying authorities and
project proponents submit comment on prior experiences with undertaking
the certification process and later determining that the proposed
federally licensed or permitted project would not result in an actual
discharge. The EPA also requested comment on whether there are specific
procedures that could be helpful in determining whether a proposed
federally licensed or permitted project will result in an actual
discharge, and how project proponents may establish for regulatory
purposes that there is no potential discharge and therefore no
requirement to pursue a section 401 certification. See 84 FR 44080. One
commenter supported allowing the certifying authority or project
proponent to determine, after the certification process is triggered,
that a section 401 certification is not required where there is no
actual or potential discharge. Another commenter expressed concern that
this would allow the project proponent to determine that a section 401
certification is no longer required if the project proponent
determines, after the section 401 certification process is triggered,
that there is no actual or potential discharge. Another commenter
stated that a project that is clearly defined early in the federal
licensing or permitting and certification processes would help project
proponents, certifying authorities, and federal agencies establish
whether there is a potential discharge, and therefore promote
compliance with section 401 obligations or clarify that 401
certification is not required. One commenter supported a process for
determining when a project with a potential for a discharge will result
in an actual discharge. A few commenters stated that a process for
determining whether or not there will be an actual discharge ignores
the statutory phrase ``may result in a discharge,'' and they asserted
that giving project proponents a role in such a process is improper
because they have no authority to find that section 401 would not
apply.
    This final rule does not provide a process for certifying
authorities or project proponents to determine whether a federally
licensed or permitted project may have a potential or actual discharge.
However, the federal agencies whose licenses or permits may be subject
to section 401 should consider whether such procedures, if incorporated
into their implementing regulations, may provide additional clarity
within their licensing and permitting programs. The EPA observes that,
if a certifying authority or project proponent determines after the
certification process is triggered that there is no actual discharge
from the proposed federally licensed or permitted project and no
potential for a discharge, there is no longer a need to request or
obtain certification. The EPA notes that ultimately the project
proponent is responsible for obtaining all necessary permits and
authorizations, including a section 401 certification. If the federal
licensing or permitting agency determines that there is a potential for
a discharge, as part of its evaluation of the proposed project, it may
not issue the federal license or permit unless a section 401
certification is granted or waived by the certifying authority. If a
project proponent requests a section 401 certification and later
asserts that section 401 does not apply, the EPA recommends that the
project proponent discuss the matter with, and provide supporting
information and documentation to, the certifying authority and the
federal agency. As provided in section 401(b) and section 121.16 of the
final rule, the EPA is available to provide technical assistance
throughout the section 401 process when requested to do so.
    The EPA has concluded that unlike other CWA regulatory provisions,
section 401 is triggered by the potential for any unqualified
discharge, rather than by a discharge of pollutants. This
interpretation, reflected in both the proposal and this final rule, is
consistent with the text of the statute

and with U.S. Supreme Court precedent. In S.D. Warren, the Court
considered whether discharges from a dam \42\ were sufficient to
trigger section 401, even if those discharges did not add pollutants to
waters of the United States. Because section 401 uses the term
discharge but the Act does not provide a specific definition for the
term,\43\ the Court applied its ordinary dictionary meaning, ``flowing
or issuing out.'' S.D. Warren Co. v. Maine Bd. of Envtl. Prot. et al.,
547 U.S. 370, 376 (2006). The Court concluded that Congress intended
this term to be broader than the term ``discharge of pollutants'' that
is used in other provisions of the Act, like section 402. See, e.g., 33
U.S.C. 1342, 1344; S.D. Warren, 547 U.S. at 380-81. For further
discussion of S.D. Warren, see section II.F.4.a.ii of this notice, and
for further discussion of discharges, see section III.A.2.a of this
notice. The Court held that discharges from the dam triggered section
401 because ``reading Sec.  401 to give `discharge' its common and
ordinary meaning preserves the state authority apparently intended.''
S.D. Warren, 547 U.S. at 387. The EPA's interpretation reflected in
this final rule is consistent with the Court's conclusion.
---------------------------------------------------------------------------

    \42\ In S.D. Warren, the Court was not asked to decide whether
the discharges from the dams were point source discharges.
    \43\ The Act provides, ``The term `discharge' when used without
qualification includes a discharge of a pollutant, and a discharge
of pollutants.'' 33 U.S.C. 1362(16).
---------------------------------------------------------------------------

    Many public commenters addressed the proposed definition of
``discharge.'' Some commenters stated that the definition of
``discharge'' in the proposed rule should not contain the word
``discharge.'' Some commenters stated that the proposed rule's
definition of discharge is unnecessary because there is no ambiguity in
that statutory term. Many commenters cited S.D. Warren to argue that
the EPA's definition of ``discharge'' was too narrow, and that the rule
should define discharge by its common meaning, ``issuing or flowing
out.'' Several commenters were concerned that if discharge was defined
as being from a point source then the discharge would need to contain
pollutants, because of the CWA definition of ``point source.'' \44\ One
commenter recommended that ``discharge'' be defined as ``the specific
outflow from a point source into navigable waters.'' Another commenter
asserted that S.D. Warren was wrongly decided and that section 401
should be triggered only by discharges of pollutants.
---------------------------------------------------------------------------

    \44\ The CWA defines point source as ``any discernible, confined
and discrete conveyance . . . from which pollutants are or may be
discharged.'' 33 U.S.C. 1362(14) (emphasis added).
---------------------------------------------------------------------------

    The EPA has considered these comments and concludes that, given the
diverse interpretations presented in public comments, including a
definition of ``discharge'' in the section 401 certification
regulations will increase clarity. Consistent with the proposal, the
Agency has concluded that a discharge need not involve pollutants in
order to trigger section 401. The EPA disagrees with commenters who
asserted that a point source discharge necessarily requires a discharge
of pollutants. The definition of point source in section 502(14) of the
CWA provides that a point source is a conveyance from which pollutants
are or may be discharged. A discharge of pollutants is not required for
a conveyance to be considered a point source. As discussed immediately
above and in section III.A.2.a of this notice, the EPA's longstanding
position is that the term ``discharge'' as used in section 401 is
limited to point sources but includes releases regardless of whether
they contain pollutants. The Agency disagrees with commenters who
stated that using the term ``discharge'' within the definition of
``discharge'' creates confusion or ambiguity. Indeed, the final rule
definition is consistent with the CWA section 502(16) definition of
``discharge,'' which also contains the term ``discharge.'' The EPA also
disagrees with commenters who asserted that the proposed definition was
narrower than the Court's opinion in S.D. Warren. As noted above, the
final rule's definition is consistent with the Court's application of
the ordinary meaning of the term. Finally, the EPA disagrees with the
commenter's recommendation to define ``discharge'' as the specific
outflow from a point source into navigable waters. The EPA has
concluded that this language could be construed quite narrowly to mean
a discharge from a specific ``outfall'' such as a pipe or outlet, while
excluding discharges from dredge or fill projects.
    One commenter requested that the EPA clarify that section 401
certification is required only where there is a discharge of pollutants
to a water of the United States, and not simply a withdrawal of water.
As discussed above, the EPA does not interpret section 401 as requiring
a discharge of pollutants. However, the EPA agrees with commenters that
a section 401 certification is not required for a water withdrawal that
has no associated potential for a point source discharge to a water of
the United States. Multiple court decisions have concluded that a water
withdrawal is not a discharge and therefore does not trigger the need
for a water quality certification.\45\
---------------------------------------------------------------------------

    \45\ See, e.g., North Carolina v. FERC, 112 F.3d 1175, 1187
(D.C. Cir. 1997) (holding that withdrawal of water from lake does
not constitute discharge for CWA section 401 purposes).
---------------------------------------------------------------------------

b. ``From a Point Source''
    The final rule provides that, to trigger section 401, a discharge
must be from a point source. Several commenters agreed that a section
401 certification is required only where there is a point source
discharge. A few commenters agreed that Title IV of the CWA focuses on
point source discharges, specifically in sections 402 and 404, leading
them to conclude that section 401 should apply only to point sources as
well. One commenter stated that the trigger for section 401 is
specifically a potential point source discharge, citing to Oregon
Natural Desert Ass'n v. Dombeck, 172 F.3d 1092 (9th Cir. 1998). Some
commenters stated that the Supreme Court in S.D. Warren held that the
certification requirement was not limited to discharges of pollutants,
but that the discharge must nonetheless be a point source discharge,
citing Dombeck. Other commenters also referred to S.D. Warren to assert
that the Supreme Court refused to limit the term ``discharge'' to only
include a point source discharge. These commenters stated that the
Supreme Court held that the term ``discharge of pollutants'' was
limited to point sources and the term ``discharge'' was significantly
broader. In doing so, many commenters took issue with the EPA's
reliance on Dombeck. One commenter cited Russello v. United States, 464
U.S. 16 (1983), to argue generically that ``when `Congress includes
particular language in one section of a statute but omits it in another
section of the same Act, it is generally presumed that Congress acts
intentionally and purposely in the disparate inclusion or exclusion.'
''
    The final rule requirement that a discharge must be from a point
source to trigger section 401 is consistent with case law from the
Ninth Circuit, which concluded that the word ``discharge'' as used
consistently throughout the CWA refers to the release from a point
source, and that use is also appropriate for section 401. Dombeck, 172
F.3d at 1099. The EPA has consistently implemented the interpretation
of section 401 articulated by the Dombeck court and adopts the Ninth
Circuit's interpretation in this final rule. The interpretation that a
discharge must be a point source discharge is consistent with the
structure of the Act and with the other

CWA regulatory programs (see section III.A.2.a of this notice).\46\
---------------------------------------------------------------------------

    \46\ See, e.g., Briefs of the United States in ONDA v. Dombeck,
Nos. 97-3506, 97-35112, 97-35115 (9th Cir. 1997), and ONDA v. USFS,
No. 08-35205 (9th Cir. 2008).
---------------------------------------------------------------------------

    The EPA disagrees with commenters who asserted that the Supreme
Court in S.D. Warren specifically addressed whether a discharge must be
from a point source. The Court's focus in S.D. Warren was on whether
pollutants must be added to constitute a ``discharge.'' S.D. Warren,
547 U.S. at 376-87. See also ONDA v. USFS, 550 F.3d 778, 783-84 (9th
Cir. 2008) (noting that ``[t]he issue in S.D. Warren was narrowly
tailored to determine whether a discharge from a point source could
occur absent addition of any pollutant to the water emitted from the
dam turbines''). The Court stated that the term discharge is broader
than ``discharge of a pollutant'' and ``discharge of pollutants,'' but
noted that ``discharge'' is not defined in the statute. S.D. Warren,
547 U.S. at 376. The Court also noted that for purposes of section 401,
``neither the EPA nor FERC has formally settled the definition, or even
set out agency reasoning,'' and the Court therefore continued to rely
on the dictionary definition of the term to mean ``flowing or issuing
out'' or ``to emit; to give outlet to; to pour forth . . .'' Id. In
2008, after the S.D. Warren decision was issued, the Ninth Circuit was
asked to revisit its 1998 decision in Dombeck. In response, the Ninth
Circuit held that ``[n]either the ruling nor the reasoning in S.D.
Warren is inconsistent with this court's treatment of nonpoint sources
in Sec.  401 of the Act, as explained in Dombeck. Accordingly, the
principles of stare decisis apply, and this court need not revisit the
issue decided in Dombeck.'' ONDA v. USFS, 550 F.3d 778, 785 (9th Cir.
2008). The Agency agrees.
    In this final rule, the EPA is formally establishing a definition
for the term ``discharge'' for purposes of CWA section 401 and setting
out its reasoning in support of the definition. The final rule's
definition is consistent with the Agency's longstanding interpretation
of the statute and with relevant Ninth Circuit case law, and nothing in
S.D. Warren or PUD No. 1 precludes the EPA from adopting the definition
in the final rule.\47\
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    \47\ On April 23, 2020, the United States Supreme Court issued a
decision in County of Maui, Hawaii v. Hawaii Wildlife Fund, et al.,
No. 18-260, which addressed the question whether the Clean Water Act
requires a NPDES permit under section 402 of the Act when pollutants
originate from a point source but are conveyed to navigable waters
by groundwater. The Court held that ``the statute requires a permit
when there is a direct discharge from a point source into navigable
waters or when there is the functional equivalent of a direct
discharge.'' Op. at 15 (emphasis in original). The Court articulated
a number of factors that may prove relevant for purposes of section
402 permitting. Id. at 16. Consistent with the Court's decision, if
a discharge of a pollutant is determined to require a federal permit
under section 402 as the functional equivalent of a direct
discharge, it will also be subject to section 401 because, as
discussed above, the term ``discharge'' under section 401 includes a
discharge of a pollutant subject to section 402. S.D. Warren Co. v.
Maine Bd. of Envtl. Prot., 547 U.S. 370, 375 (2006) (citing 33
U.S.C. 1362(16)). This conclusion is consistent with the Court's
decision in Maui.
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c. ``Into a Water of the United States''
    Consistent with the proposal, the final rule reflects that section
401 is triggered by a potential discharge into a water of the United
States. 33 U.S.C. 1341(a)(1), 1362(7). Potential discharges into State
or Tribal waters that are not waters of the United States do not
trigger the requirement to obtain section 401 certification. Id. at
1342(a)(1).
    Many commenters agreed that certification is required where there
is a discharge into a water of the United States. Some of these
commenters agreed that section 401 would not apply to non-federal
waters. A couple of commenters expressed concern that by limiting the
requirement for a section 401 certification to activities that
discharge directly to waters of the United States, there would be many
federally permitted projects where section 401 certification would not
be required even though discharges from those projects could impact
State or Tribal waters. A few commenters argued that the EPA's
deference to States has been inconsistent, noting that the Agency's
proposed rulemaking to define ``waters of the United States'' placed
strong emphasis on States' authority to protect their water resources,
while the proposed section 401 rulemaking reduces States' authority to
protect their water resources. These commenters said that they had
difficulty reconciling the States' expanded role under the ``waters of
the United States'' rule with the diminished role of States in the
proposed rule.
    The final rule's interpretation that a discharge must be into a
water of the United States to trigger the section 401 certification
requirement is consistent with the plain text of the statute, is
supported by the legislative history, and is consistent with other CWA
regulatory program requirements that apply to discharges to waters of
the United States, not discharges to State or Tribal waters. Id.; see
also H.R. Rep. No. 92-911, at 124 (1972) (``It should be clearly noted
that the certifications required by section 401 are for activities
which may result in any discharge into navigable waters.'') (emphasis
added); see also section III.A.2.a of this notice for discussion on
discharges to waters of the United States. The EPA disagrees with
commenters who suggested that this rule is inconsistent with the
recently finalized rule defining ``waters of the United States.'' Both
rules are intended to provide clarity on the scope of federal authority
and State or Tribal authority to regulate certain waters. The final
definition of ``waters of the United States'' reestablishes the
appropriate balance between waters subject to federal regulation and
those waters or features that are subject to exclusive State or Tribal
jurisdiction. As described further in section II.F of this notice,
section 401 provides a role for States and authorized Tribes to
participate in federal license or permitting processes, including those
in which they may otherwise be preempted by federal law. States and
Tribes retain authority to regulate and protect waters of the State or
Tribe in accordance with State and Tribal law and where not preempted
by federal law. As explained in detail in the proposed rule preamble,
section 401 is a federal regulatory provision, as certification
conditions are incorporated into federal licenses and permits and are
enforceable by the federal government. If section 401 was expanded to
cover activities with discharges to non-federal waters, such an
expansion would authorize the federal government to regulate waters and
features that are beyond the scope of CWA regulatory authority;
Congress did not intend these waters to be subject to federal
regulation.
d. Federal License or Permit
    Section 401 certification requirements are triggered when a project
proponent applies for a federal license or permit to conduct an
activity which may result in any discharge into a water of the United
States. 33 U.S.C. 1341(a)(1). However, in those cases where a federal
agency discharges dredged or fill material into waters of the United
States but does not issue itself a license or permit, the Corps'
regulations require reasonable and appropriate efforts to demonstrate
compliance with effluent limitations and state water quality standards,
which typically includes seeking certification.\48\ Consistent with the

proposal, the final rule defines the term ``license or permit'' to mean
``any license or permit granted by an agency of the Federal Government
to conduct any activity which may result in a discharge.''
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    \48\ See Appendix C of Engineer Regulation 1105-2-100; 33 CFR
335.2 (``[T]he Corps does not issue itself a CWA permit to authorize
Corps discharges of dredged material or fill material into U.S.
waters, but does apply the 404(b)(1) guidelines and other
substantive requirements of the CWA and other environmental
laws.'').
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    The CWA does not list specific federal licenses and permits that
are subject to section 401 certification requirements. The EPA believes
that the most common examples of licenses or permits that may be
subject to section 401 certification are CWA section 402 NPDES permits
issued by EPA in States where the EPA administers the NPDES permitting
program; CWA section 404 permits for the discharge of dredged or fill
material and Rivers and Harbors Act sections 9 and 10 permits issued by
the Army Corps of Engineers; and hydropower and interstate natural gas
pipeline licenses issued by FERC. The final rule does not provide an
exclusive list of federal licenses and permits that may be subject to
section 401. Instead, the final rule focuses on whether there is
potential for the activity authorized by the federally issued license
or permit to result in a discharge from a point source into a water of
the United States.
    A few commenters requested clarification on the requirement for a
federal license or permit to trigger the need for a section 401
certification. One commenter asserted that the proposal was unclear
because the proposed regulatory text did not tie the need for a section
401 certification to an application for a federal license or permit.
The EPA disagrees with the suggestion that the proposal does not tie
the need for a section 401 certification to the application for a
federal license or permit. Section 121.2 of the proposed rule stated
that ``any applicant for a license or permit to conduct any activity
which may result in a discharge shall provide the Federal agency a
certification from the certifying authority . . .'' As noted above, the
proposal and this final rule define the term ``license or permit'' as
one issued by a federal agency.
    A few commenters suggested that additional language be added to the
proposed definition of ``discharge'' to clearly describe what
constitutes a point source, including language concerning equipment and
construction activities associated with the discharge of dredged or
fill material. The EPA believes that defining ``point source'' in the
final rule is unnecessary in light of the statutory definition (33
U.S.C. 1362(14)) and court decisions concluding that bulldozers,
mechanized land clearing machinery, and similar types of equipment used
for discharging dredge or fill material are ``point sources.'' \49\
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    \49\ See, e.g., Avoyelles Sportsmen's League v. Marsh, 715 F.2d
897 (5th Cir. 1983); U.S. v. Larkins, 657 F.Supp. 76 (W.D. Kent.
1987), aff'd, 852 F.2d 189 (6th Cir. 1988).
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    Another commenter asserted that States have required facilities to
obtain a section 401 certification where the facility has a permit from
a State with delegated authority under section 402. Section 401
certification is not required for State- or Tribally-issued permits
when the State or Tribe has assumed operation of the permit program in
lieu of the federal government.\50\ The CWA statutory language is clear
that the license or permit triggering the need for a section 401
certification must be a federal license or permit, that is, one issued
by a federal agency. Implementation of a State or Tribal permit program
in lieu of the federal program does not ``federalize'' the resulting
licenses or permits for purposes of section 401. Section 401
certification does not apply to those authorizations issued by the
State or Tribe.\51\ The CWA anticipates that States and Tribes issuing
those permits will ensure consistency with CWA provisions and other
appropriate requirements of State and Tribal law as part of their
permit application evaluation.
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    \50\ State or Tribal implementation of a license or permit
program in lieu of the federal program, such as a CWA section 402
permit issued by an authorized state, does not federalize the
resulting licenses or permits and therefore does not trigger section
401 certification. This conclusion is supported by the legislative
history of CWA section 401, which noted that ``since permits granted
by States under section 402 are not Federal permits--but State
permits--the certification procedures are not applicable.'' H.R.
Rep. No. 92-911, at 127 (1972). The legislative history of the CWA
amendments of 1977, discussing state assumption of section 404, also
noted that ``[t]he conferees wish to emphasize that such a State
program is one which is established under State law and which
functions in lieu of the Federal program. It is not a delegation of
Federal authority.'' H.R. Rep. No. 95-830, at 104 (1977).
    \51\ As described elsewhere in this notice, the Corps' existing
certification regulations provide a reasonable period of time of 60
days for federally issued CWA section 404 permits. 33 CFR
325.2(b)(1)(ii); see also final rule preamble section III.F. To the
extent that certifying authorities believe that this timeline is too
short to provide certification for a Federally issued section 404
permit, States are authorized to assume administration of that
program for certain waters. 40 CFR 233; see also Final Report of the
Assumable Waters Subcommittee (May 2017), available at https://www.epa.gov/cwa404g/nacept-assumable-waters-subcommittee-final-report-may-10-2017.
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    One commenter noted that the proposal indicated that the Corps does
not process and issue permits for its own activities and stated that
federal agencies should be subject to the same certification request
submittal requirements as non-federal agency project proponents. In
response, the EPA notes that the CWA ties the requirement for a section
401 certification to a federal license or permit. As a result, in
circumstances where there is no federal license or permit, including
when federal agency activities do not require a license or permit,
section 401 certification is not required. Nonetheless, the Corps'
current regulations indicate that section 401 requires the Corps to
seek section 401 certification for dredge and fill projects involving a
discharge into waters of the United States, regardless of whether the
Corps issues itself a permit for those activities.\52\
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    \52\ See 33 CFR 336.1(a)(1) (``The CWA requires the Corps to
seek state water quality certification for discharges of dredged or
fill material into waters of the U.S.'').
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B. Pre-Filing Meeting Request

1. What is the Agency finalizing?
    The EPA proposed to establish a pre-filing meeting process when the
EPA is the certifying authority to ensure that the Agency receives
early notification of anticipated projects and can discuss information
needs with the project proponent. Many commenters stated that it would
be helpful for project proponents to request pre-filing meetings with
all certifying authorities (not just the EPA), although most commenters
did not say that certifying authorities should be required to accept
such meetings. In light of these comments, and because the benefits of
the pre-filing process are applicable regardless of the identity of the
certifying authority, the EPA is finalizing a requirement that all
project proponents, including federal agencies when they seek
certification for general licenses or permits, submit a request for a
meeting with the appropriate certifying authority at least 30 days
prior to submitting a certification request.\53\ The final rule
requires only that the project proponent request the pre-filing meeting
and leaves to the discretion of the certifying authority whether a pre-
filing meeting may be

necessary or appropriate for a particular project. The meeting request
itself provides advance notification to the certifying authority that a
certification request may be forthcoming and therefore promotes early
coordination, even when the certifying authority does not hold a pre-
filing meeting.
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    \53\ The EPA recognizes that some activities conducted in
response to a hurricane or other similar event may require emergency
procedures that do not allow for compliance with pre-request meeting
procedures. Federal licensing and permitting agencies should
establish such emergency procedures by regulation to ensure that
project proponents, certifying authorities, and the public are made
aware of the types of circumstances that could prevent compliance
with ordinary pre-filing meeting request requirements. Nothing in
this final rule precludes federal agencies from establishing
emergency procedures to ensure continuation of operations or other
appropriate emergency procedures, including procedures that may not
allow for compliance with pre-request meeting procedures.
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2. Summary of Final Rule Rationale and Public Comment
    The EPA is expanding the proposed pre-filing meeting request
requirement, and under this final rule, all project proponents,
including federal agencies when they seek certification for general
licenses or permits, must submit a request for a pre-filing meeting
with the appropriate certifying authority at least 30 days prior to
submitting a certification request. This requirement will ensure that
certifying authorities receive early notification and have an
opportunity to discuss the project and potential information needs with
the project proponent before the statutory timeframe for review begins.
The final rule also encourages the certifying authority to take actions
to initiate coordination with the Federal agency after receiving the
pre-filing meeting request.
    In order to facilitate early engagement and coordination, and using
its discretion to interpret the term ``request'' as applied to
certification procedures, the EPA is finalizing a regulatory
requirement in section 121.4 of the final rule that all project
proponents must submit a request for a pre-filing meeting at least 30
days in advance of submitting a certification request. Under the final
rule, certifying authorities are given an opportunity to accept or host
such a pre-filing meeting, but they retain discretion to decline the
request or simply not respond. Under the final rule, if the certifying
authority does not respond to the request, the project proponent may
submit a certification request as long as it includes documentation, as
required in section 121.5 of the final rule, that it requested the pre-
filing meeting at least 30 days prior to submitting the certification
request.
    In addition to requiring the project proponent to request a pre-
filing meeting, the proposed rule would have required EPA to respond
within a certain period of time and also required the parties to
discuss certain topics and to be prepared to share certain information
during the pre-filing meeting. The final rule no longer requires those
additional procedures and instead encourages certifying authorities,
project proponents and federal licensing and permitting agencies to
engage in early coordination. Under the final rule, if the certifying
authority grants the pre-filing meeting, the project proponent and the
certifying authority are encouraged to discuss the nature of the
proposed project and potential water quality effects. The final rule
also encourages the project proponent to provide a list of other
required State, interstate, Tribal, territorial, and federal
authorizations and to describe the anticipated timeline for
construction and operation. After receiving the pre-filing meeting
request, the certifying authority is encouraged to contact the federal
agency and to identify points of contact, so as to facilitate
information sharing between the certifying authority and Federal agency
throughout the certification process. In the final rule, the EPA
encourages these important steps to help promote an efficient
certification process. These recommendations are consistent with many
recommendations in EPA's 2019 Guidance (which EPA is rescinding in this
action, as no longer necessary in light of this final rule) as well as
with recommendations made in the proposed rule preamble.
    The Agency believes that the term ``request'' as used in the
statute is broad enough to include an implied requirement that, as part
of the submission of a request for certification, a project proponent
also provide the certifying authority with advance notice that a
certification request is imminent. The relatively short time (no longer
than one year and possibly much less) that certifying authorities are