Full opinion text
OPINION AND ORDER KENNETH M. KARAS, District Judge: In the context of water regulation, federal law provides that “the discharge of any pollutant by any person shall be unlawful.” 33 U.S.C. § 1311(a). And, as relevant here, it defines a “discharge of a pollutant” to mean “any addition of any pollutant to navigable waters from any point source.” Id. § 1362(12). The Environmental Protection Agency (“EPA”) interprets these provisions not to apply to a “water transfer,” which it has defined, in a regulation, to mean “an activity that conveys or connects waters of the United States without subjecting the transferred water to intervening industrial, municipal, or commercial use.” 40 C.F.R. § 122.3(i). Before the Court are multiple motions and cross-motions for summary judgment challenging or defending this regulation as promulgated under the Clean Water Act (“CWA”), 33 U.S.C. §§ 1251 et seq., and the Administrative Procedure Act (“APA”), 5 U.S.C. §§ 551 et seq. As with many things legal and nautical, there is much complexity to confront below the surface of this seemingly simple language. Let’s dive in. I. Background A. Statutory History Congress has long sought to protect the integrity of our Nation’s waters by limiting what we put in them. In 1899, it passed the Rivers and Harbors Act, which made it unlawful, in part, “to throw, discharge, or deposit ... from or out of any ... floating craft of any kind, or from the shore ... any refuse matter of any kind or description whatever ... into any navigable water of the United States, or into any tributary of any navigable water.... ” Rivers and Harbors Appropriations Act of 1899, ch. 425, § 13, 30 Stat. 1152 (codified as amended at 33 U.S.C. § 407). In addition to limiting the “discharge ... [of] refuse matter,” the Act authorized the Secretary of the Army, acting pursuant to the judgment of the Army Corps of Engineers, to “permit the deposit of any material above mentioned in navigable waters, within limits to be defined and under conditions to be prescribed by him.” Id. Almost fifty years later, Congress significantly expanded its water-regulation authority when it passed the Federal Water Pollution Control Act of 1948, ch. 758, Pub.L. No. 845, 62 Stat. 1155 (codified as amended at 33 U.S.C. §§ 1251 et seq.). This Act provided, inter alia, that [t]he pollution of interstate waters in or adjacent to any State or States (whether the matter causing or contributing to such pollution is discharged directly into such waters or reaches such waters after discharge into a tributary of such waters), which endangers the health or welfare of persons in a State other than that in which the discharge originates, is hereby declared to be a public nuisance and subject to abatement as herein provided. Id. § 2(d)(1). Although the Act did not define “pollution,” it did define “interstate waters” to mean “all rivers, lakes, and other waters that flow across, or form a part of, State boundaries.” Id. § 10(e). This part of the Act was slightly amended in 1956, see ch. 518, Pub.L. No. 660, § 8(a), 70 Stat. 498, and it was again amended in 1961 to expand the scope of the regulation from “interstate waters” to “interstate or navigable waters,” see Pub.L. No. 87-88, § 8(a), 75 Stat. 204 (“The pollution of interstate or navigable waters in or adjacent to any State or States ... which endangers the health or welfare of any persons, shall be subject to abatement_”). The 1961 amendments also modified the definition of “interstate waters,” but it did not define the newly added term “navigable waters.” See id. § 9(e) (“The term ‘interstate waters’ means all rivers, lakes, and other waters that flow across or form a part of State boundaries, including coastal waters.”). Then, about a decade later, Congress passed the Federal Water Pollution Control Act Amendments of 1972 (“1972 Amendments”), Pub.L. No. 92-500, 86 Stat. 816 (codified as amended at 33 U.S.C. §§ 1251 et seq.), which represented a “comprehensive revision of national water quality policy.” S.Rep. No. 95-370, at 1 (1977), 1977 U.S.C.C.A.N. 4326, 4327. As relevant here, § 301 of the amended Act provided that, “[e]xcept as in compliance with” certain sections of the Act, “the discharge of any pollutant by any person shall be unlawful.” Id. § 301(a), 86 Stat. at 844 (codified as amended at 33 U.S.C. § 1311(a)). Separately, the Act defined “discharge of a pollutant” to mean, in relevant part, “any addition of any pollutant to navigable waters from any point source.” Id. § 502(12), 86 Stat. at 886 (codified as amended at 33 U.S.C. § 1362(12)). It further defined “pollutant” to mean “dredged spoil, solid waste, incinerator residue, sewage, garbage, sewage sludge, munitions, chemical wastes, biological materials, radioactive materials, heat, wrecked or discarded equipment, rock, sand, cellar dirt and industrial, municipal, and agricultural waste discharged into water.” Id. § 502(6), 86 Stat. at 886 (codified as amended at 33 U.S.C. § 1362(6)). It also defined “point source” to mean “any discernible, confined and discrete conveyance, including but not limited to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, ... or vessel or other floating craft, from which pollutants are or may be discharged.” Id. § 502(14), 86 Stat. at 887 (codified as amended at 33 U.S.C. § 1362(14)). Finally, the Act defined “navigable waters” to mean “the waters of the United States, including the territorial seas.” Id. § 502(7), 86 Stat. at 886 (codified as amended at 33 U.S.C. § 1362(7)). In addition to significantly revising federal water-quality standards, Congress, through § 402 of the Act, created the National Pollutant Discharge Elimination System (“NPDES”). See id. § 402, 86 Stat. at 880-83 (codified as amended at 33 U.S.C. § 1342). Under this program, which explicitly replaced the permit program previously established by the Rivers and Harbors Act of 1899, see id. § 402(a)(5), 86 Stat. at 880 (codified as amended at 33 U.S.C. § 1342(a)(5)), the Administrator of the EPA “may ... issue a permit for the discharge of any pollutant[ ] ... notwithstanding [§ ]301(a), upon condition that such discharge will meet ... such conditions as the Administrator determines are necessary to carry out the provisions of this Act.” Id. § 402(a)(1), 86 Stat. at 880 (codified as amended at 33 U.S.C. § 1342(a)(1)). After obtaining a permit, any person discharging pollutants in compliance with the permit’s terms is deemed to comply with § 301(a)’s ban on pollutant discharges. Id. § 402(k), 86 Stat. at 883 (codified as amended at 33 U.S.C. § 1342(k)). But in addition to providing federal authority to issue permits, Congress also provided state governments with authority to create their own permit programs that, once established, would supersede the EPA’s ability to issue permits in that state. Specifically, § 402 provides that “the Governor of each State desiring to administer its own permit program for discharges into navigable waters within its jurisdiction may submit to the Administrator a full and complete description of the program it proposes to establish and administer under State law or under an interstate compact.” Id. § 402(b), 86 Stat. at 880-82 (codified as amended at 33 U.S.C. § 1342(b)). Thereafter, “the Administrator shall suspend the issuance of permits ... as to those navigable waters subject to such program unless he [or she] determines [within ninety days of the State’s submission] that the State permit program does not meet ... or does not conform to” various requirements and guidelines in the Act. Id. § 402(c)(1), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(c)(1)). Once established, however, the Administrator must continually monitor the state program to ensure that it remains in compliance with the Act. Id. §§ 402(c)(2)-(3), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(c)(2)-(3)) (providing that “[a]ny State permit program under this section shall at all times be in accordance with this section and [other] guidelines,” and that “[whenever the Administrator determines ... that a State is not administering a program approved' under this section in accordance with requirements of this section, he shall so notify the State and, if appropriate corrective action is not taken within a reasonable time, ... the Administrator shall withdraw approval of such program”). And the Administrator may object to, and thereby block, the issuance of any permit pursuant to a state program. Id. § 402(d), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(d)). Or the Administrator may waive his or her ability to object to a single permit application, see id. § 402(d)(3), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(d)(3)), or to a category of permit applications, see id. § 402(e), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(e)) (waiver of objections to categories of point sources); id. § 402(f), 86 Stat. at 882 (codified as amended at 33 U.S.C. § 1342(f)) (authority to “promulgate regulations establishing categories of point sources which [the Administrator] determines shall not be subject to the [approval] requirements” of § 402(d)). Following the 1972 Amendments, Congress enacted another significant set of Amendments five years later when it passed the Clean Water Act of 1977 (“1977 Amendments”), Pub.L. No. 95-217, 91 Stat. 1566 (codified as amended at 33 U.S.C. §§ 1251 et seq.). Although these amendments did not substantially alter the NPDES program under § 402, the pollutant-discharge limitation under § 301(a), or the definitions of any of the previously discussed statutory terms defined in § 502, they did add a policy statement to § 101’s “Declaration of Goals and Policy.” Where the 1972 Amendments provided that “[t]he objective of th[e] Act is to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters,” 1972 Amendments § 101(a), 86 Stat. at 816 (codified as amended at 33 U.S.C. § 1251(a)), and that “[i]t is the policy of the Congress to recognize, preserve, and protect the primary responsibilities and rights of States to prevent, reduce, and eliminate pollution, to plan the development and use ... of land and water resources, and to consult with the Administrator in the exercise of his [or her] authority,” id. § 101(b), 86 Stat. at 816 (codified as amended at 33 U.S.C. § 1251(b)), the 1977 Amendments added § 101(g), providing that “[i]t is the policy of Congress that the authority of each State to allocate quantities of water within its jurisdiction shall not be superseded, abrogated or otherwise impaired by th[e] Act,” 1977 Amendments § 5(a), 91 Stat. at 1567 (codified as amended at 33 U.S.C. § 101(g)). Taken together, these provisions of the CWA — prohibiting pollutant discharges, establishing the NPDES program, defining key terms, and clarifying congressional policy goals — comprise the relevant statutory framework within which the Court analyzes the instant Motions. But we have only just gotten our feet wet. The Court will now proceed to discuss EPA’s history of administering and interpreting the Act as it relates to the present case. B. Regulatory History 1. “Navigable Waters ” As discussed, the CWA defines “navigable waters” to mean “the waters of the United States.” 33 U.S.C. § 1362(7). In this context, EPA’s interpretation of the scope of its regulatory authority over the Nation’s waters has evolved over time, but, in general, it represents an expansion of the statutory concept of “navigable waters.” Initially, in the immediate aftermath of Congress’s passage of the 1972 Amendments, EPA interpreted “navigable waters” to match precisely the statutory phrase. See 37 Fed.Reg. 28,390, 28,392 (Dec. 22, 1972) (formerly codified at 40 C.F.R. § 124.1(n)) (“The definition!] of [‘navigable waters’] contained in [§ ] 502 of the Act shall be applicable to sueh terms as used in this part_”). Soon thereafter, EPA’s Office of the General Counsel published a memorandum concluding, based on a review of the legislative history of the 1972 Amendments, that, in defining “navigable waters” to mean “the waters of the United States,” Congress intended that the statute “eliminate[] the requirement of navigability,” but also that “pollution of waters covered by the bill must be capable of affecting interstate commerce.” Memorandum from the EPA Office of the General Counsel on Water Pollution, at *1 (Feb. 6, 1973), available at 1973 WL 21937 (EPA Office of the General Counsel). The memorandum then noted that the Agency would face “a major task to determine, on a case by ease basis, what waters fall within” the statutory category, but it proposed that at least the following waters would appear to be “waters of the United States”: (1) All navigable waters of the United States; (2) Tributaries of navigable waters of the United States; (3) Interstate waters; (4) Interstate lakes, rivers, and streams which are utilized by interstate travelers for recreational or other purposes; (5) Interstate lakes, rivers, and streams from which fish or shellfish are taken and sold in interstate commerce; and (6) Interstate lakes, rivers, and streams which are utilized for industrial purposes by industries in interstate commerce. Id. EPA subsequently adopted the memorandum’s recommended interpretation of “navigable waters” in a 1973 rulemaking, noting that, in the newly adopted regulation, “[t]he definition of ‘navigable waters’ ha[d] been clarified by incorporating additional language.” See 38 Fed.Reg. 13,528, 13,528-29 (May 22, 1973) (codifying the memorandum’s proposed interpretation at 40 C.F.R. § 125.1(0)). Approximately two years later, the EPA’s Office of the General Counsel again issued a memorandum — this time in the form of a formal opinion — discussing the scope of “navigable waters” as applied to the question of whether discharges of pollutants from “irrigation return flows” required permits under the NPDES program. See In re Riverside Irrigation Dist., Ltd. & 17 Others (June 27, 1975), available at 1975 WL 23864 (EPA Office of the General Counsel, Opinion No. 21). Although the Opinion’s conclusion rested primarily on its determination that an irrigation return flow is a “point source” subject to NPDES permit requirements, see id. at *2-3, it also discussed its interpretation of “navigable waters” in response to a claim that, if an irrigation return flow were determined to be a “navigable water,” it would not be subject to regulation as a “point source.” First, it reaffirmed the 1973 memorandum’s case-by-case approach for determining whether any individual water fit within the statutory framework, declining to deem irrigation ditches as a category to be “navigable waters,” and instead concluding that “the waters that are the subject of these permits may well be determined by the finder of fact, applying the statutory and regulatory test to the facts of these cases, to be navigable waters within the definition of the Act.” Id. at *4. Second, it noted that, even if “any given irrigation ditch [were determined to be] a navigable water, it would still be permittable as a point source where it discharges into another navigable water body_” Id. (emphasis in original). Third, it recognized that the term “navigable waters” encompassed not only entire bodies of water but also individual portions of those bodies, stating that “[i]t is clear that the intent of Congress in adopting this definition of ‘navigable waters’ was to broaden the concept of navigable waters to ‘portions thereof, tributaries thereof ... and the territorial seas and the Great Lakes.’” Id. at *3 (second alteration in original) (emphasis removed) (quoting United States v. Holland, 373 F.Supp. 665, 671 (M.D.Fla.1974)). Fourth, and most importantly, it defended EPA’s broad interpretation of the scope of “navigable waters” while explicitly basing its ability to expand this scope on Congress’s intent that EPA would have broad permitting authority over pollution discharges: The clear tenor of the legislative history ... is that the broad definition of “navigable waters” serves to expand the application of the Act and the permit program, not narrow it.... [T]o define the waters here at issue as navigable waters and use that as a basis for exempting them from the permit requirement appears to fly directly in the face of clear legislative intent to the contrary. Id. at *4. In other words, in its determination that pollutant-discharging point sources that could also be classified as “navigable waters” would still be subject to NPDES permitting requirements, the Opinion foreclosed the possibility that it could interpretively expand the scope of “navigable waters” in a way that restricted its permitting authority. Subsequent regulations continued to clarify the expansive scope of “navigable waters” by focusing less on the “navigability” component and more on the “interstate commerce” component. In a 1979 rule-making, EPA codified a definition of “navigable waters” that it claimed was “slightly revised to clarify its intent and scope,” but faithful to “the basic thrust and coverage” of the previous definition. 44 Fed.Reg. 32,854, 32,858 (June 7, 1979). Per the new regulation, [w]aters [would] be considered to be waters of the United States not only if they [we]re actually used, but also if they [could] be susceptible to use, for industrial purposes by industries in interstate commerce. Thus the regulations [focused], not on the nature of the stream’s users, but on the characteristics of the stream itself, and it [would] no longer be necessary to show actual industrial use for a stream to fall within the definition. Id. Pursuant to the new focus on potential use in interstate commerce, the regulation defined “navigable waters” to include “[a]ll waters which are currently used, were used in the past, or may be susceptible to use in interstate or foreign commerce,” and “[a]ll other waters ... the use, degradation or destruction of which would affect or could affect interstate or foreign commerce.” Id. at 32,901 (previously codified at 40 C.F.R. § 122.3(t)). Moreover, to reinforce the declining emphasis on “navigability,” EPA noted in a comment included in the newly codified definition that, “[f]or purposes of clarity the term ‘waters of the United States’ is primarily used throughout the regulations rather than ‘navigable waters.’ ” Id. Following the 1979 rulemaking and, in particular, the rulemaking’s nod toward replacing “navigable waters” with “waters of the United States” throughout the regulations, EPA eliminated its definition of “navigable waters” while reappropriating that definition’s language to define the statutory phrase “waters of the United States.” See 45 Fed.Reg. 33,290, 33,298 (May 19, 1980) (“ ‘[N]avigable waters’ ... now appears as the definition of “Waters of the United Statesf ]’.... ”). Currently, after a reorganization of the NPDES regulations in 1983, see 48 Fed.Reg. 14,146 (Apr. 1, 1983), EPA’s definition of “waters of the United States” appears in 40 C.F.R. § 122.2, which provides, in relevant part: Waters of the United States or waters of the U.S. means: (a) All waters which are currently used, were used in the past, or may be susceptible to use in interstate or foreign commerce, including all waters which are subject to the ebb and flow of the tide; (b) All interstate waters, including interstate “wetlands;” (c) All other waters such as intrastate lakes, rivers, streams (including intermittent streams), mudflats, sandflats, “wetlands,” sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds the use, degradation, or destruction of which would affect or could affect interstate or foreign commerce including any such waters: (1) Which are or could be used by interstate or foreign travelers for recreational or other purposes; (2) From which fish or shellfish are or could be taken and sold in interstate or foreign commerce; or (3) Which are used or could be used for industrial purposes by industries in interstate commerce; (d) All impoundments of waters otherwise defined as waters of the United States under this definition; (e) Tributaries of waters identified [above]; (f) The territorial sea; and (g) “Wetlands” adjacent to waters ... identified [above]. 40 C.F.R. § 122.2. Throughout this regulatory evolution of the EPA’s interpretation of its permitting authority, the Supreme Court remained relatively silent. However, in United States v. Riverside Bayview Homes, Inc., 474 U.S. 121, 106 S.Ct. 455, 88 L.Ed.2d 419 (1985), it finally dipped its oar in the water. In that case, the Supreme Court confronted the Army Corps of Engineers’ (“the Corps’ ”) assertion of permitting authority over discharges of a pollutant into a “wetland,” which assertion the Corps had made under § 404 of the CWA — a provision that, like § 402, allowed the Corps (instead of EPA) to issue permits for discharges into “navigable waters” as defined in § 502(7). See 33 U.S.C. § 1344(a) (“The Secretary [of the Corps] may issue permits ... for the discharge of dredged or fill material into the navigable waters at specified disposal sites.”). In holding that the Corps’ expansive definition of “navigable waters” to include “wetlands” was “a permissible interpretation of the [CWA],” the Supreme Court held that Congress chose to define the waters covered by the Act broadly. Although the Act prohibits discharges into “navigable waters,” the Act’s definition of “naviga- ■ ble waters” as “the waters of the United States” makes it clear that the term “navigable” as used in the Act is of limited import. In adopting this definition of “navigable waters,” Congress evidently intended to repudiate limits that had been placed on federal regulation by earlier water pollution control statutes and to exercise its powers under the Commerce Clause to regulate at least some waters that would not be deemed “navigable” under the classical understanding of that term. Riverside Bayview, 474 U.S. at 133, 106 S.Ct. 455 (citations omitted). And in accepting the Corps’ expansive interpretation of “navigable waters,” the Supreme Court explicitly relied on “the evident breadth of congressional concern for protection of water quality and aquatic ecosystems,” specifically holding that, [i]n view of the breadth of federal regulatory authority contemplated by the Act itself and the inherent difficulties of defining precise bounds to regulable waters, the Corps’ ecological judgment about the relationship between waters and their adjacent wetlands provides an adequate basis for a legal judgment that adjacent wetlands may be defined as waters under the Act. Id. at 133-34, 106 S.Ct. 455. Although Riverside Bayview did not directly evaluate EPA’s similarly expansive interpretation of “navigable waters,” its holding was in line with EPA’s view that its broad authority over “navigable waters” flowed from Congress’s intent to expand EPA’s authority to prohibit and, where appropriate, to permit pollutant discharges. The Supreme Court made a splash again over a decade later in Solid Waste Agency of Northern Cook County v. U.S. Army Corps of Engineers ("SWANCC”), 531 U.S. 159, 121 S.Ct. 675, 148 L.Ed.2d 576 (2001), wherein it limited “navigable waters” as defined in Riverside Bayview not to encompass the Corps’ new interpretation, which defined “navigable waters” to include a “seasonally ponded, abandoned gravel min[e] ... used as [a] habitat by migratory bird[s].” Id. at 164-65, 121 S.Ct. 675 (internal quotation marks omitted). Although the Supreme Court had previously held that “the term navigable as used in the [CWA] is of limited import,” Riverside Bayview, 474 U.S. at 133, 106 S.Ct. 455, the Court in SWANCC clarified that “Congress’ separate definitional use of the phrase ‘waters of the United States’ [did not] constitutef] a basis for reading the term ‘navigable waters’ out of the statute,” 531 U.S. at 172, 121 S.Ct. 675. Instead, it noted that it is one thing to give a word limited effect and quite another to give it no effect whatever. The term ‘navigable’ has at least the import of showing us what Congress had in mind as its authority for enacting the CWA: its traditional jurisdiction over waters that were or had been navigable in fact or which could reasonably be so made. Id. It thus found that the Corps’ interpretation was foreclosed by the statute, and it rejected the Corps’ attempt further to expand the scope of “navigable waters.” See id. at 174, 121 S.Ct. 675 (“We hold that [the Corps’ interpretation of ‘navigable waters’] ... exceeds the authority granted to [the Corps] under § 404(a) of the CWA.”). Again, the Supreme Court’s holding did not apply directly to the EPA’s interpretation. But the EPA subsequently endorsed the Supreme Court’s approach in SWANCC in a regulation specifying that “[t]he determination of whether a particular cooling pond is or is not ‘waters of the United States’ is to be made by the permit writer on a case-by-case basis, informed by the principles announced in” that case. See 66 Fed.Reg. 65,256, 65,259 (Dec. 18, 2001). 2. The Water Transfers Rule Somewhat parallel to the regulations and cases defining the scope of “navigable waters,” EPA began to clarify — through positions it took in various court cases — its interpretation of its permitting authority over pollutant discharges resulting from transfers of water within and between navigable waters. In National Wildlife Federation v. Gorsuch, 693 F.2d 156 (D.C.Cir.1982), EPA defended its policy of not requiring a permit to transfer water through a dam against the argument that the “release of polluted water through [a] dam into [a] downstream river constitutes the ‘addition’ of a pollutant to navigable waters ‘from’ a point source” under § 502(12), triggering EPA’s “nondiscretionary duty to regulate” the discharges under § 402. Id. at 165. It argued, instead, that “for [an] addition of a pollutant from a point source to occur, the point source must introduce the pollutant into navigable water from the outside world; dam-caused pollution, in contrast, merely passes through the dam from one body of navigable water ... into another.” Id. The D.C. Circuit, according “great deference” to the EPA, id. at 166 (internal quotation marks omitted), accepted this interpretation, holding that it was “reasonable” and “not inconsistent with congressional intent,” id. at 183. Similarly, as an amicus curiae in National Wildlife Federation v. Consumers Power Co., 862 F.2d 580 (6th Cir.1988), EPA made many of the same arguments it had made in Gorsuch to support a power company defending itself from the claim that it was required to obtain an NPDES permit to operate a hydroelectric dam. Like the D.C. Circuit in Gorsuch, the Sixth Circuit deferred to EPA’s interpretation in holding that “no pollutant is introduced from the outside world ... because any [pollutant] released with the ... water originatefd] in [a navigable water], and [did] not enter the [receiving navigable water] from the outside world.” Id. at 585. In so holding, the court also joined the D.C. Circuit in holding that Congress did not intend to regulate dams as “point sources.” See id. at 587-88 (citing 33 U.S.C. § 1314(f)(2)(F); Gorsuch, 693 F.2d at 177). But, because the dams in Consumers Power — which removed, held, and altered water — were arguably distinguishable from the dams in Gorsuch — which “were ... located within navigable waters ... [and] merely pass[ed] on water of already altered quality,” id. at 589 (internal quotation marks omitted) — the Sixth Circuit offered an additional rationale for excluding the dams at issue from the NPDES program: The water which passes through the [dam] never loses its status as water of the United States.... The [dam’s] movement or diversion of water from [a navigable water] into a storage reservoir is distinguishable from the diversion of waters of the United States by industrial operations for cooling purposes in which the water loses its status as water of the United States. The [dam] merely changes the movement, flow, or circulation of navigable waters when it temporarily impounds waters ... in a storage reservoir, but does not alter their character as waters of the United States. On the other hand, steam/electric industrial operations remove water, which then enters the industrial complex and absorbs heat and other minerals produced by the plant or electric generator before being added to waters of the United States. Id. The Sixth Circuit thus distinguished between dams, which it had followed the D.C. Circuit in holding were non-point sources of pollution “generally not subject to the NPDES permit requirements,” id. at 590, and industrial operations, which subjected the water to industrial use before discharging it back into navigable waters. In the wake of Gorsuch and Consumers Power, other courts refused to extend these decisions outside the context of dams in cases not directly involving the EPA. In Dague v. City of Burlington, 935 F.2d 1343 (2d Cir.1991), rev’d in part on other grounds, 505 U.S. 557, 112 S.Ct. 2638, 120 L.Ed.2d 449 (1992), the Second Circuit held that water transferred between two navigable bodies of water through a “railroad culvert” constituted a “discharge of a pollutant” because the culvert met the statute’s definition of a “point source.” See id. at 1355. And in Dubois v. U.S. Department of Agriculture, 102 F.3d 1273 (1st Cir.1996), the First Circuit held that a ski resort’s transfer of water from a river into a pond via a system of pumps and pipes used to make snow was a “discharge of a pollutant” into the pond because “the pipe discharging the water into [the pond was] a point source,” and the river and the pond were “not the same body of water.” Id. at 1296-97. Moreover, in contrast to the Sixth Circuit in Consumers Power, the First Circuit held that the water “lost its status as waters of the United States” during the transfer because “the water [left] the domain of nature and [was] subject to private control rather than purely natural processes.” Id. at 1297. Finally, in Catskill Mountains Chapter of Trout Unlimited, Inc. v. City of New York (“Catskills I”), 273 F.3d 481 (2d Cir.2001), the Second Circuit held that New York City’s transfer of water from a reservoir to a creek — both “navigable waters” — via a tunnel — which “plainly qualifíe[d] as a point source,” id. at 493 — resulted in the “discharge of a pollutant” without a permit, in violation of § 301(a). See id. at 494. The Second Circuit distinguished its holding from Gorsuch and Consumers Power in two ways. First, it held that EPA’s interpretation — on which the City relied — did not deserve deference because it “had [not] been adopted in a rulemaking or other formal proceeding,” but was instead “based on a series of informal policy statements ... and ... litigation positions.” Id. at 490. Second, although it agreed with EPA’s and other courts’ interpretation that an “addition” of a pollutant required that the pollutant be introduced “from the outside world,” it defined the “outside world” to be “any place outside the particular water body to which pollutants are introduced.” Id. at 491 (internal quotation marks omitted). Thus, whereas “Gorsuch and Consumers Power essentially involved the recirculation of water” through a dam, id. at 491, the situation the Second Circuit confronted “strain[ed] past the breaking point the assumption of ‘sameness’” made in those cases because the water was “artificially diverted from its natural course and travelled] several miles from the [reservoir] through [the tunnel] to [the creek], a body of water utterly unrelated in any relevant sense to the [reservoir],” id. at 492. Thus, the Second Circuit in Catskills I followed its prior decision in Bague and the First Circuit’s decision in Dubois in holding that the transfer of water between two distinct navigable bodies of water through a point source required a permit under § 402. See id. at 492-93. A few years after Catskills I, the Supreme Court addressed the water-transfer issue in South Florida Water Management District v. Miccosukee Tribe of Indians (“SFWMD”), 541 U.S. 95, 124 S.Ct. 1537, 158 L.Ed.2d 264 (2004). In that case, the Miccosukee Tribe challenged the operation of a pumping facility that transferred water from a canal into a nearby reservoir without an NPDES permit. See id. at 98, 124 S.Ct. 1537. Initially, the Court rejected the argument that § 301(a) covers only pollutants originating from a point source, holding instead that “a point source need not be the original source of the pollutant; it need only convey the pollutant to ‘navigable waters.’ ” Id. at 105, 124 S.Ct. 1537. Then, the Supreme Court proceeded to address the argument — made for the first time in the Government’s amicus brief— that “all the water bodies that fall within the [CWA’s] definition of ‘navigable waters’ ... should be viewed unitarily for purposes of NPDES permitting requirements,” and thus that “such permits are not required when water from one navigable water body is discharged, unaltered, into another navigable water body.” Id. at 105-06, 124 S.Ct. 1537 (first emphasis added) (some internal quotation marks omitted). The Court ultimately declined to resolve whether this interpretation — which it called the “unitary waters” approach— was consistent with the statute, holding that EPA’s interpretation did not deserve deference because the government “[had] not identified] any administrative documents in which EPA ha[d] espoused that position,” id. at 107, 124 S.Ct. 1587, and that the parties had failed to raise this argument in their memoranda to the courts below or in their petitions for certiorari, id. at 109, 124 S.Ct. 1537. Instead, because both parties conceded that a permit would not be required if the canal and the reservoir were “simply two parts of the same water body,” id., it remanded the case for a determination of whether the canal and the reservoir were “meaningfully distinct water bodies,” id. at 112, 124 S.Ct. 1537 — a factual determination that the district court had made prematurely at the summary-judgment stage, id. at 111, 124 S.Ct. 1537. In light of the Second Circuit’s decision in Catskills I and the Supreme Court’s decision in SFWMD, both of which declined to defer to EPA’s interpretation of § 301(a) in the context of a water transfer, EPA in 2005 took the first step toward formalizing- its interpretation. In a memorandum issued from the EPA’s Office of \ a <^eneral c°unsel to all Regional EPA to^strators-referred to as the “Klee EPA Gmf^ J3ecause i1; was issued by EPA General Counsel Ann R. Klep_wpA concluded, after an analysis of the CWA’s language, its legislative history, and relevant case law, that “Congress intended to leave the oversight of water transfers to authorities other than the NPDES program.” (Administrative Record (“AR”) 5, at 19 (Memorandum from Ann R. Klee to EPA Regional Administrators on Agency Interpretation on Applicability of Section 402 of the Clean Water Act to Water Transfers (Aug. 5, 2005)).) In clarifying language, the Memorandum defined a “water transfer” as “any activity that conveys or connects navigable waters ... without subjecting the water to intervening industrial, municipal, or commercial use.” (Id. at 1.) And while the Memorandum explicitly “[did] not address the meaning of the terms[ ] ‘point source,’ ‘pollutant’ or ‘navigable waters,’ ” (id. at 18 n. 19), it based its conclusion instead entirely on the statutory term “addition,” (see id. at 18), which it interpreted using a “holistic view” of the statute, “[giving] meaning to those statutory provisions where Congress expressly considered the issue of water resource management, as well as Congress’ overall division of responsibility between State and federal authorities under the statute,” (id. at 13). The Memorandum also addressed EPA’s aforementioned 1975 formal opinion in which it concluded that pollutant discharges from irrigation ditches required NPDES permits, noting that “th[e] opinion did not specifically address the question of whether an ‘addition’ has occurred when a navigable water is merely conveyed to another navigable water,” and that the .opinion’s practical effect was overridden by subsequent legislation specifically exempting irrigation return flows from regulation. (Id. at 2-3 n. 5 (citing 33 U.S.C. § 1342(i )(1) (“The Administrator shall not require a permit under this section for discharges composed entirely of Return flows from irrigated agriculture ■ •.. ”); id. § 1362(14) (“Th[e] term [point source] does not include ... return flows from irrigated agriculture.”))-) It otherwise concluded that, “[t]o the extent the 1975 [o]pinion ... conflicts with this Agency interpretation with respect to water transfers, it is superseded.” (Id.) After the Supreme Court decided SFWMD and after EPA issued the Klee Memorandum, the Second Circuit was confronted with an opportunity to reconsider its holding in Catskills I in an appeal from a district court order (issued after the remand in Catskills I) granting summary judgment against the City of New York and assessing a civil penalty for failing to obtain an NPDES permit. See Catskill Mountains Chapter of Trout Unlimited, Inc. v. City of New York (“Catskills II”), 451 F.3d 77, 80 (2d Cir.2006). Holding that the Supreme Court’s decision in SFWMD supported its decision in Catskills I, id. at 83, and accepting the City’s concession that the EPA’s interpretation as expressed in the Klee Memorandum did not deserve Chevron deference, id. at 82, the Second Circuit reaffirmed its holding in Catskills I, id. Notably, in so doing, it criticized the Klee Memorandum’s “ ‘holistic’ arguments about the allocation of state and federal rights” in the CWA because those arguments “simply overlooked] [the CWA’s] plain language,” which requires that EPA “balance” the “seemingly inconsistent goals” of “achievfing] water allocation goals as well as ... restoring] and maintain[ing] the quality of the nation’s waters.” Id. at 84-85. It thus rejected EPA’s interpretation, which “tipfped] the balance toward allocation goals,” in favor of “honoring ... the balance that Congress has struck and remains free to change.” Id. at 85. Approximately one week before the Second Circuit decided Catskills II, EPA initiated notice-and-comment rulemaking on a proposed rule codifying the Klee Memorandum’s position that transfers of water between navigable bodies of water do not require NPDES permits. See 71 Fed.Reg. 32,887 (June 7, 2006). EPA received over 18,000 comments on the rule, (see AR 1428 at 3 (Response to Public Comments: National Pollutant Discharge Elimination System (NPDES) Water Transfers Final Rule (40 C.F.R. Part 122); Docket #: EPA-HQ-OW-2006-0141)), and it responded to the issues raised by these comments in a document filed as part of the Administrative Record, (see id.). Then, on June 13, 2008, EPA issued its final rule, adding, as an “exclusion” to the NPDES program, “[discharges from a water transfer.” See 73 Fed.Reg. 33,697, 33,708 (June 13, 2008) (codified at 40 C.F.R. § 122.3(f)). Thus, pursuant to the Water Transfers Rule, EPA’s regulations currently read, in relevant part: The following discharges do not require NPDES permits: (i) Discharges from a water transfer. Water transfer means an activity that conveys or connects waters of the United States without subjecting the transferred water to intervening industrial, municipal, or commercial use. This exclusion does not apply to pollutants introduced by the water transfer activity itself to the water being transferred. 40 C.F.R. § 122.3(f). C. Procedural History These two rivers of regulatory history — ■ the scope of “navigable waters” and the Water Transfers Rule — have now converged in this Action, where the Court must decide whether EPA’s interpretation of the statute sinks or swims. Wasting no time after EPA issued the final rule on June 13, 2008, one group of plaintiffs— which the Court will refer to as the “Environmental Plaintiffs” — filed a Complaint less than one week later against the agency and its Administrator (collectively, “EPA”). (See Dkt. No. 1 (08-CV-5606 Dkt.) (Compl., filed on June 20, 2008).) Separately, another group of plaintiffs— which the Court will refer to as the “State Plaintiffs” — filed a Complaint a few months later, also against EPA. (See Dkt. No. 1 (08-CV-8430 Dkt.) (Compl., filed on Oct. 2, 2008).) On October 8, the Court granted the State Plaintiffs’ request to consolidate both cases. (See Dkt. No. 18 (08-CV-5606 Dkt.) (entered Oct. 10, 2008).) At approximately the same time that the actions were filed in this Court, a number of parallel actions were filed in other courts, some by Parties to this Consolidated Action. See, e.g., Env’t Am. v. EPA No. 08-1853 (1st Cir.); Jones River Watershed Ass’n v. EPA No. 08-2322 (1st Cir.); Catskill Mountain Chapter of Trout Unlimited, Inc. v. EPA No. 08-3203 (2d Cir.); New York v. EPA No. 08-8444 (2d Cir.); Pennsylvania v. EPA, No. 08-4178 (3d Cir.); Mich. Chapter of Trout Unlimited, Inc. v. EPA, No. 08-4366 (6th Cir.); Sierra Club v. EPA No. 08-14921 (11th Cir.); Miccosukee Tribe of Indians of Fla. v. EPA No. 08-13652 (11th Cir.); Fla. Wildlife Fed’n v. EPA No. 08-13657 (11th Cir.); Friends of the Everglades v. EPA No. 08-CV-21785 (S.D.Fla.); Miccosukee Tribe of Indians of Fla. v. EPA, No. 08-CV-021858 (S.D.Fla.); Rivers Coal. Def. Fund, Inc. v. EPA 08-CV-80922 (S.D.Fla.). “On July 22, 2008, pursuant to 28 U.S.C. § 2112(a)(3), the United States Judicial Panel on Multidistrict Litigation ... consolidated the five petitions for review of the Water Transfers Rule then pending in the First, Second, and Eleventh Circuit Courts of Appeal and randomly assigned them to the Eleventh Circuit.” Catskill Mountains Chapter of Trout Unlimited, Inc. v. U.S. E.P.A., 630 F.Supp.2d 295, 304 (S.D.N.Y.2009). The Eleventh Circuit then “granted in part the parties’ joint motion to consolidate those petitions,” consolidated a sixth petition for review, and stayed all of those petitions pending disposition of the appeal of Friends of the Everglades v. South Florida Water Management District, No. 07-13829-HH (11th Cir.), a separate but conceptually related case filed in August 2007 and on appeal to the Eleventh Circuit. Id. The District Court for the Southern District of Florida also stayed proceedings in its case pending disposition of that appeal. Id. at 304 n. 6. In December 2008, EPA filed a Motion To Stay or, in the alternative, To Dismiss the Case for lack of subject-matter jurisdiction in light of both the Friends of the Everglades appeal and the consolidated petitions. (See Dkt. No. 28 (Mot.); Dkt. No. 29 (Mem. of Law in Supp. of Defs.’ Mot. for Stay or, in the Alternative, To Dismiss).) On April 29, 2009, the Court granted the Motion To Stay “pending the Eleventh Circuit’s resolution of Friends of the Everglades and the Consolidated Petitions.” Catskill Mountains, 630 F.Supp.2d at 307. Two months later, the Eleventh Circuit decided the appeal in Friends of the Everglades, applying Chevron deference to the Water Transfers Rule and reversing the district court’s ruling that the water transfer at issue required an NPDES permit. See Friends of the Everglades v. S. Fla. Water Mgmt. Dist. (‘Friends I"), 570 F.3d 1210, 1228 (11th Cir.2009). But, in September 2012, because the Eleventh Circuit had not yet resolved the Consolidated Petitions, the Court placed this Case on the Suspense Calendar. (See Dkt. No. 79.) Then, on October 26, 2012, the Eleventh Circuit issued an opinion dismissing the consolidated petitions for lack of subject-matter jurisdiction under 33 U.S.C. § 1369(b)(1). See Friends of the Everglades v. U.S. E.P.A. (“Friends II"), 699 F.3d 1280 (11th Cir.2012). Thereafter, pursuant to this Court’s Order, the Stay lifted on December 17, 2012, when the Eleventh Circuit’s mandate dismissing the case was scheduled to issue. (See Dkt. No. 84.) Subsequently, a number of other plaintiffs and defendants waded into the case when, after a pre-motion conference held on January 30, 2013, the Court granted, on the Parties’ consent, multiple applications to intervene as plaintiffs and defendants under Rule 24 of the Federal Rules of Civil Procedure. (See Dkt. No. 114.) This added, as Intervenor-Plaintiffs, the Micco-sukee Tribe of Indians of Florida, Friends of the Everglades, the Florida Wildlife Federation, and the Sierra Club (collectively, “Environmental Intervenor-Plain-tiffs”), and, as Intervenor-Defendants, Alaska, Arizona, Colorado, Idaho, Nebraska, Nevada, New Mexico, North Dakota, Texas, Utah, and Wyoming (collectively, “State Intervenor-Defendants”); South Florida Water Management District (“SFWMD”); and multiple municipal water providers from western states (“Western Water Providers”). (See id.) In joining the case as intervenors, these Parties followed the City of New York, which previously joined as an Intervenor-Defendant after the Court granted its Rule 24 Motion To Intervene in October 2008. (See Dkt. No. 22). At the same time that it granted the Parties’ applications to intervene, the Court also adopted a briefing schedule, whereby the Parties could file motions and cross-motions to dismiss or for summary judgment. (See Dkt. No. 114.) Initially, both EPA and SFWMD filed motions to dismiss for lack of subject matter jurisdiction, arguing that, pursuant to 33 U.S.C. § 1369(b)(1), and contrary to the Eleventh Circuit’s ruling in Friends II, this Court did not have original jurisdiction over the Complaint. (See Dkt. No. 122 (EPA’s Mot.); Dkt. No. 125 (SFWMD’s Mot.).) However, pursuant to a later Stipulation of Dismissal, the Court dismissed these Motions without prejudice pending further action by the Supreme Court on the Eleventh Circuit’s decision, which decision the Parties acknowledged had collateral-estop-pel effect. (See Dkt. No. 154.) The Supreme Court ultimately declined to hear the appeal. See U.S. Sugar Corp. v. Friends of the Everglades, — U.S.-, 134 S.Ct. 422, 187 L.Ed.2d 280 (2013); Envmtl. Prot. Agency v. Friends of the Everglades, — U.S.-, 134 S.Ct. 421, 187 L.Ed.2d 280 (2013); S. Fla. Water Mgmt. Dist. v. Friends of the Everglades, — U.S.-, 134 S.Ct. 422, 187 L.Ed.2d 280 (2013). Prior to the Supreme Court’s denial of certiorari and pursuant to the Court’s January 2013 scheduling order, the Parties submitted multiple Motions and Cross-motions for Summary Judgment. (See Dkt. No. 136 (Envtl. Pis.’ Mot. for Summ. J.); Dkt. No. 142 (Envtl. Intervenor-Pls.’ Joint Mot. for Summ. J.); Dkt. No. 148 (State Pis.’ Mot. for Summ. J.); Dkt. No. 158 (EPA’s Cross-Mot. for Summ. J.); Dkt. No. 165 (SFWMD’s Cross-Mot. for Summ. J.); Dkt. No. 167 (City of New York’s Mot. for Summ. J.); Dkt. No. 170 (State Intervenor-Defs.’ Mot. for Summ. J.); Dkt. No. 174 (Western Water Providers’ Cross-Mot. for Summ. J.).) These Motions were fully submitted as of August 2013. (See Dkt.) Thus, after it received notice of the certiorari denial, the Court scheduled oral argument on the motions, (see Dkt. No. 216), which hearing it held on December 19, 2013, (see Dkt. No. 219 (Hr’g Tr.)). Having held oral argument, and after reviewing thoroughly the Parties’ submissions and the Administrative Record, the Court is now ready to resolve the Motions. II. Discussion A. Legal Standard 1. Summary Judgment Summary judgment shall be granted where it is shown “that there is no genuine dispute as to any material fact and the movant is entitled to judgment as a matter of law.” Fed.R.Civ.P. 56(a); see also Celotex Corp. v. Catrett, 477 U.S. 317, 322-23, 106 S.Ct. 2548, 91 L.Ed.2d 265 (1986) (same). ‘When ruling on a summary judgment motion, the district court must construe the facts in the light most favorable to the non-moving party and must resolve all ambiguities and draw all reasonable inferences against the movant.” Dali. Aerospace, Inc. v. CIS Air Corp., 352 F.3d 775, 780 (2d Cir.2003). Where a court reviews agency action under the APA, “[sjummary judgment ... serves as the mechanism for deciding, as a matter of law, whether the agency action is supported by the administrative record and is otherwise consistent with the APA standard of review.” Bennett v. Donovan, 4 F.Supp.3d 5, 8, 2013 WL 5424708, at *2 (D.D.C. Sept. 30, 2013); see also Physicians Comm. for Responsible Med. v. Johnson, 436 F.3d 326, 331 (2d Cir.2006) (resolving conflict over agency action and interpretation of a statute in the context of cross-motions for summary judgment); Consumer Fed’n of Am. & Pub. Citizen v. U.S. Dep’t of Health & Human Servs., 83 F.3d 1497, 1501 (D.C.Cir.1996) (same). Thus, “[wjhere, as here, a party seeks review of agency action under the APA and the entire case on review is a question of law, summary judgment is generally appropriate.” Noroozi v. Napolitano, 905 F.Supp.2d 535, 541 (S.D.N.Y.2012) (internal quotation marks omitted); see also Just Bagels Mfg., Inc. v. Mayorkas, 900 F.Supp.2d 363, 372 (S.D.N.Y.2012) (“When a party seeks review of agency action under the APA, ... judicial review of agency action is often accomplished by filing cross-motions for summary judgment.” (internal quotation marks and alterations omitted)). 2. Review of Agency Rulemaking “The fair measure of deference to an agency administering its own statute has been understood to vary with circumstances,” and this understanding “has produced a spectrum of judicial responses, from great respect at one end ... to near indifference at the other.” United States v. Mead Corp., 533 U.S. 218, 228, 121 S.Ct. 2164, 150 L.Ed.2d 292 (2001) (citations omitted). In certain circumstances, an agency’s interpretation of a statute “is ‘entitled to respect’ only to the extent it has the ‘power to persuade.’ ” Gonzales v. Oregon, 546 U.S. 243, 256, 126 S.Ct. 904, 163 L.Ed.2d 748 (2006) (quoting Skidmore v. Swift & Co., 323 U.S. 134, 140, 65 S.Ct. 161, 89 L.Ed. 124 (1944)). But, where, as here, “Congress has unambiguously vested [an agency] with general authority to administer [a statute] through rulemaking ... and the agency interpretation at issue was promulgated in the exercise of that authority,” the Court analyzes the agency’s interpretation under the two-step framework established in Chevron, U.S.A, Inc. v. Natural Res. Def. Council, Inc., 467 U.S. 837, 104 S.Ct. 2778, 81 L.Ed.2d 694 (1984). City of Arlington v. F.C.C., — U.S. -, 133 S.Ct. 1863, 1874, — L.Ed.2d - (2013). At step one, the Court asks “whether Congress has directly spoken to the precise question at issue.” Chevron, 467 U.S. at 842, 104 S.Ct. 2778. “If the intent of Congress is clear, ... the court, as well as the agency, must give effect to the unambiguously expressed intent of Congress.” Id. at 842-43, 104 S.Ct. 2778. However, where the statute “simply does not speak with the precision necessary to say definitively whether it applies” to the precise question, United States v. Eurodif S.A., 555 U.S. 305, 319, 129 S.Ct. 878, 172 L.Ed.2d 679 (2009), the Court “must uphold the [agency’s] judgment as long as it is a permissible construction of the statute, even if it differs from how the court would have interpreted the statute in the absence of an agency regulation,” Sebelius v. Auburn Reg’l Med. Ctr., — U.S. -, 133 S.Ct. 817, 826, 184 L.Ed.2d 627 (2013). The agency’s interpretation is thus “binding in the courts unless procedurally defective, arbitrary or capricious in substance, or manifestly contrary to the statute.” Mead, 533 U.S. at 227, 121 S.Ct. 2164. B. Chevron Step One To determine “whether Congress has directly spoken to the precise question at issue,” Chevron, 467 U.S. at 842, 104 S.Ct. 2778, it is first necessary to define the precise question. The Water Transfers Rule merely adds “[discharges from a water transfer” to its list of NPDES “[exclusions.” 40 C.F.R. § 122.3(i). Reading this text in isolation, the rule arguably addresses the precise question whether Congress intended to require NPDES permits for water transfers as defined by the rule — or, put differently, whether Congress intended to allow EPA to decide whether to exclude water transfers from NPDES regulation. But if this were the question, then EPA would lose at step one, because courts have consistently held that EPA does not have statutory authority to create NPDES exclusions. See, e.g., Nw. Envtl. Advocates v. U.S. E.P.A., 537 F.3d 1006, 1021-22 (9th Cir.2008) (holding that “[§ ] 402 allows the [EPA] to issue a permit, but it does not provide that the [EPA] may entirely exempt certain categories of discharges from the permitting requirement” — a conclusion that “EPA [did] not seriously contest”); N. Plains Res. Council v. Fid. Exploration & Dev. Co., 325 F.3d 1155, 1164 (9th Cir.2003) (“EPA does not have the authority to exempt discharges otherwise subject to the CWA. Only Congress may amend the CWA to create exemptions from regulation.”); Natural Res. Def. Council, Inc. v. Costle, 568 F.2d 1369, 1377 (D.C.Cir.1977) (“The wording of the statute, legislative history, and precedents are clear: the EPA Administrator does not have authority to exempt categories of point sources from the permit requirements of [§ ]402.”); see also Decker v. Nw. Envtl. Def. Ctr., — U.S.-, 133 S.Ct. 1326, 1331, 185 L.Ed.2d 447 (2013) (noting, without comment, the D.C. Circuit’s holding in Costle “that the [CWA] did not give the EPA ‘authority to exempt categories of point sources from the permit requirements’ of the Act” (quoting Costle, 568 F.2d at 1377)). Consequently, EPA claims to have answered the broader question whether Congress intended to prohibit water transfers generally under § 301(a), such that water transfers would be subject to regulation under NPDES, among other programs. (See EPA’s Mem. of Law in Opp’n to Pis.’ & Intervenor Pis.’ Mots, for Summ. J. & in Supp. of the Federal Defs.’ Cross-Mot. for Summ. J. (“EPA Mem.”) (Dkt. No. 173) 24 (“[T]he statutory question at issue is whether the NPDES regime extends to water transfers in the first place.”); id. at 36 n. 11 (“EPA in promulgating the Water Transfers Rule did not create a regulatory exemption, but rather exercised its inherent authority to interpret ambiguous provisions of a statute administered by the agency.”); EPA’s Reply Mem. of Law in Supp. of Its Cross-Mot. for Summ. J. (“EPA Reply”) (Dkt. No. 206) 3 (“EPA at no point ‘created,’ nor indeed presumed to have the authority to create, any exemptions from the NPDES permitting scheme that were not already contained within the CWA. Rather, EPA interpreted the CWA applying traditional principles of statutory construction, and concluded that the CWA itself, as reasonably interpreted, excludes certain water transfers from NPDES permitting requirements. The Water Transfers Rule, therefore, merely clarifies the relevant ambiguous statutory provisions in manner [sic] consistent with EPA’s longstanding practice.”); AR 1428 at 11 (“[T]he principal issue in [the Water Transfers Rule] is not whether EPA may exempt from NPDES permit obligations a class of entities responsible for the discharge of a pollutant, but the conditions under which one would properly have a discharge of a pollutant.”).) Because § 301(a) provides that “the discharge of any pollutant by any person shall be unlawful,” 33 U.S.C. § 1311(a), the question then becomes whether a water transfer, as defined by the rule, is a “discharge of a pollutant.” That question, in turn, requires an analysis of § 502(12), which defines “discharge of a pollutant” to mean, in relevant part, “any addition of any pollutant to navigable waters from any point source.” Id. § 1362(12). The focal point of the Court’s Chevron-step-one analysis, therefore, is whether Congress clearly answered the precise question whether a transfer of water and any pollutants contained therein is an “addition” of those pollutants “to navigable waters.” See 73 Fed.Reg. 33,700 (“The legal question addressed by [the Water Transfers Rule] is whether a water transfer as defined in the new regulation constitutes an ‘addition’ within the meaning of section 502(12).”). (See AR 5 at 2 & n. 3 (“The precise legal question addressed here is whether the movement of pollutants from one navigable water to another by a water transfer is the ‘addition’ of a pollutant potentially subjecting the activity to the permitting requirement under section 402 of the Act.”).) If Congress clearly intended not to consider water transfers to be “addition[s] ... to navigable waters” under § 502(12), then it would follow that EPA has authority to adopt a regulation “excluding” water transfers from programs that regulate such “additions,” in-eluding the NPDES program. But if Congress clearly intended EPA to consider water transfers to be “addition[s] ... to navigable waters,” then the Water Transfer Rule would violate the statute. And if it were unclear whether Congress intended either interpretation, then it would follow that EPA could use its general delegation of authority to “prescribe such regulations as are necessary to carry out [its] functions under” the CWA to choose an interpretation of § 502(12) that does not include water transfers, thereby allowing EPA to promulgate a regulation “exempting” them from the NPDES program. 33 U.S.C. § 1361(a) (“The Administrator is authorized to prescribe such regulations as are necessary to carry out his [or her] functions under [the CWA].”); see also 73 Fed.Reg. 33,698 (“This final rule is issued under the authority of sections 402 and 501 of the Clean Water Act[,] 33 U.S.C. [§§ ]1342[,] 1361.”). The focal point of the step-one analysis, therefore, is whether Congress directly spoke to the issue of whether a water transfer is an “addition ... to navigable waters” under § 502(12). “Because the judiciary functions as the final authority on issues of statutory construction, an agency is given no deference at all on the question whether a statute is ambiguous.” Wells Fargo Bank, N.A. v. F.D.I.C., 310 F.3d 202, 205-06 (D.C.Cir.2002) (internal quotation mark’s and alterations omitted). It is thus the Court’s task to determine, at step one, whether Congress has answered the “precise question at issue.” See Vill. of Barrington, Ill. v. Surface Transp. Bd., 636 F.3d 650, 659-60 (D.C.Cir.2011) (“Because at Chevron step one we alone are tasked with determining the Congress’s unambiguous intent, we answer [the step-one question] without showing the agency any special deference.”). This determination requires a multipart analysis. First, the Court asks whether “[any] court’s prior judicial construction of [the] statute” conflicts with EPA’s interpretation. Nat’l Cable & Telecomm. Ass’n v. Brand X Internet Servs., 545 U.S. 967, 982, 125 S.Ct. 2688, 162 L.Ed.2d 820 (2005). If such a conflicting interpretation “followed] from the unambiguous terms of the statute,” such that the court specifically held “that the statute unambiguously forecloses the agency’s interpretation,” then that court’s interpretation “displaces [the] conflicting agency construction” and the analysis ends at step one. Id. at 982-83, 125 S.Ct. 2688. However, if the court merely identified the “best reading” of the statute, but not the “only permissible reading,” id. at 984, 125 S.Ct. 2688, then this Court must employ “traditional tools of statutory construction [to] ascertain[] [whether] Congress had an intention on the precise question at issue,” Chevron, 467 U.S. at 843 n. 9, 104 S.Ct. 2778. In conducting this analysis, the Court should “begin with the statutory text” of §§ 301(a) and 502(12). Cohen v. JP Morgan Chase & Co., 498 F.3d 111, 116 (2d Cir.2007). Then, “[i]f the statutory language is ambiguous ... [the Court] [would] resort first to canons of statutory construction, and, if the [statutory] meaning remains ambiguous, to legislative history, to see if these interpreti