Northwest Environmental Advocates v. United States Environmental Protection Agency

Plaintiffs in this case are Northwest Environmental Advocates, San Francisco Baykeeper, and The Ocean Conservancy. Plaintiffs-intervenors are the States of Illinois, Michigan, Minnesota, New York, Pennsylvania, and Wisconsin. Plaintiffs and plaintiffs-intervenors challenge a regulation originally promulgated by the Environmental Protection Agency (“EPA”) in 1973 exempting certain marine discharges from the permitting scheme of sections 301(a) and' 402 of the Clean Water Act (“CWA”). That regulation, 40 C.F.R. § 122.3(a), provides that the following vessel discharges into the navigable waters of the United States do not require permits: discharge of effluent from properly functioning marine engines; discharge of laundry, shower, and galley sink wastes from vessels; and any other discharge incidental to the normal operation of a vessel, including the discharge of ballast water.

The district court concluded that the EPA had exceeded its authority under the CWA in exempting these discharges from permitting requirements. The district court vacated § 122.3(a), effective September 30, 2008. We affirm the decision of the district court.

I. Background

A. The CWA and 40 C.F.R. § 122.3(a)

In 1972, Congress enacted sweeping amendments to the Federal Water Pollution Control Act of 1948. After another round of substantial amendments in 1977, the statute became known as the Clean Water Act. The CWA declares a “national goal that the discharge of pollutants into the navigable waters be eliminated by 1985.” 33 U.S.C. § 1251(a)(1).

Section 301(a) of the CWA provides that, subject to certain exceptions, “the discharge of any pollutant by any person shall be unlawful.” Id. § 1311(a). One of these exceptions is for discharges authorized by a permit granted pursuant to the National Pollutant Discharge Elimination System (“NPDES”), a system set forth in section 402 of the Act. Id. §§ 1311(a), 1342. The combined effect of sections 301(a) and 402 is that “[t]he CWA prohibits the discharge of any pollutant from a point source into navigable waters of the United States without an NPDES permit.” N. Plains Res. Council v. Fid. Exploration & Dev. Co., 325 F.3d 1155, 1160 (9th Cir.2003). The EPA administers the NPDES. 33 U.S.C. § 1251(d).

Obtaining a permit under the CWA need not be an onerous process. For example, in appropriate circumstances a discharge may be allowed under a “general permit” requiring only that the discharger submit a “notice of intent” to make the discharge. As we explained in Natural Resources Defense Council v. U.S. EPA, 279 F.3d 1180, 1183 (9th Cir.2002):

NPDES permits come in two varieties: ■individual and general. An individual permit authorizes a specific entity to discharge a pollutant in a specific place and is issued after an informal agency adjudication process. See 40 C.F.R. §§ 122.21, 124.1-124.21, 124.51-124.66. *1011 General permits, on the other hand, are issued for an entire class of hypothetical dischargers in a given geographical region and are issued pursuant to administrative rulemaking procedures. See id. §§ 122.28, 124.19(a). General permits may appropriately be issued when the dischargers in the geographical area to be covered by the permit are relatively homogenous. See id. § 122.28(a)(2). After a general permit has been issued, an entity that believes it is covered by the general permit submits a “notice of intent” to discharge pursuant to the general permit. Id. § 122.28(b)(2). A general permit can allow discharging to commence upon receipt of the notice of intent, after a waiting period, or after the permit issuer sends out a response agreeing that the discharger is covered by the general permit. Id. § 122.28(b)(2)(iv).

In 1973, the EPA exempted by regulation several categories of vessel discharges from NPDES permitting requirements under the CWA. See NPDES, 38 Fed.Reg. 13,528, 13,530, § 125.4 (May 22, 1973). The regulation provides that “[t]he following discharges do not require NPDES permits”:

Any discharge of sewage from vessels, effluent from properly functioning marine engines, laundry, shower, and galley sink wastes, or any other discharge incidental to the normal operation of a vessel. This exclusion does not apply to rubbish, trash, garbage, or other such materials discharged overboard; nor to other discharges when the vessel is operating in a capacity other than as a means of transportation^]

40 C.F.R. § 122.3(a). The CWA expressly exempts sewage discharges from vessels from the permitting process and regulates these discharges by other means. See 33 U.S.C. §§ 1362(6)(A), 1322. Because § 122.3(a) does not itself exempt sewage discharges but instead merely recognizes the statute’s exemption of sewage discharges, the sewage clause in § 122.3(a) is not subject to the ultra vires claim made here. See also Chevron U.S.A., Inc. v. Hammond, 726 F.2d 483, 493 n. 13 (9th Cir.1984) (contrasting the express statutory exemption of sewage with regulation relating to “deballasting” by ships). Therefore, three categories of discharges exempted by 40 C.F.R. § 122.3(a) are at issue in this case: (1) marine engine discharges; (2) graywater discharges (“laundry, shower, and galley sink wastes”); and (3) “any other discharge incidental to the normal operation of a vessel.”

The first proposed draft of the regulation would have excluded only marine engine discharges. See NPDES, 38 Fed. Reg. 1362, 1363-64, § 125.4(c) (proposed Jan. 11, 1973). The EPA subsequently added the exclusions for graywater and other discharges incidental to normal vessel operations. When promulgating the final regulation in May 1973, the EPA explained its anticipated effect: “Most discharges from vessels to inland waters are now clearly excluded from the permit requirements.” 38 Fed.Reg. at 13,528, (b)(13)(ii). The EPA stated that “[t]his type of discharge generally causes little pollution.” Id. The EPA stated, further, that the “exclusion of vessel wastes from the permit requirements will reduce administrative costs drastically.” Id. Decades later, an EPA administrator declared that in 1973:

[W]e were faced with many, many other much higher priority situations such as raw sewage being discharged, municipal plants having to be built, very large paper mills or steel mills and the like discharging. At the time we thought that was not an important area to deal with.... Vessels were not important to the overall scheme of things at that time.

*1012 Craig Vogt, EPA, EPA Pub. Meeting # 12227, Ocean Discharge Criteria (Sept. 12, 2000, 1 p.m.). The EPA amended the regulation in 1979 in minor respects that do not affect our analysis. See NPDES, Revision of Regulations, 44 Fed.Reg. 32,-854, 32,902, § 122.4 (June 7, 1979); see also NPDES, Revision of Existing Regulations, 43 Fed.Reg. 37,078, 37,079, 1(c)(2) (Aug. 21, 1978) (describing the proposed changes).

The text of the CWA does not exempt from NPDES requirements marine engine discharges, graywater discharges, or other discharges incidental to the normal operation of vessels. However, the EPA contended in 1973, and continues to contend, that it has the power to provide these exemptions by regulation. The Administrator of the EPA prefaced the draft January 1973 regulation with a statement that a discharger could discharge lawfully only if the discharger “possesses a valid permit or is excluded from coverage by law or regulation.” NPDES, 38 Fed.Reg. at 1362 (emphasis added). The final rules similarly stated that “[a]ll discharges of pollutants ... are unlawful ..., unless the discharger has a permit or is specifically relieved by law or regulation from the obligation of obtaining a permit.” NPDES, 38 Fed.Reg. at 13,531, § 125.11(a) (emphasis added).

The first category exempted by § 122.3(a), marine engine discharges, includes unburned fuel and various kinds of oil. The second category, graywater discharges, can include pathogens such as fecal coliform, enterococci, and E. coli and pollutants such as ammonia, arsenic, copper, lead, nickel, and zinc. See, e.g., EPA Draft Cruise Ship Discharge Assessment Report (Dee.2007), available at http:// www.epa.gov/owow/oceans/cruise_ships/ pdf_disch_assess/ cruiseship_discharge_as-sessment_report.pdf. The third category, “any other discharge,” includes, among other discharges, ballast water from ships. Cf. 33 U.S.C. § 1322(a)(12)(A)(i) (defining this broad “other discharge” category for purposes of a different CWA section).

Plaintiffs have made clear, both here and in the district court, that their primary environmental concern stems from the discharge of ballast water. We quote a passage from the district court’s order granting plaintiffs’ motion for permanent injunctive relief that describes the purpose of ballast water and the effects of its discharge:

Ballast water is water that is taken on by cargo ships to compensate for changes in the ship’s weight as cargo is loaded or unloaded, and as fuel and supplies are consumed. Ballast water may be used for a number of different purposes, such as maintaining stability, maintaining proper propeller and bow immersion, and to compensate for off-center weights. Thus, ballast water is essential to the proper functioning of cargo ships, as well as to the safety of its crew.

Because ballast water is primarily used to compensate for changes in cargo, it is generally taken in or pumped out at the ports along a ship’s route. When a ship takes on ballast water, whether freshwater or saltwater, organisms found in that water are typically taken in as well. These organisms are carried in the ballast tanks of the ship until the ship arrives at its next port, where, due to changes in the distribution of the ship’s cargo, they may be released into a new ecosystem. Due to the size of ballast tanks on modern cargo ships, and the speed with which these ships can reach their destinations, organisms are increasingly able to survive the journey to a new ecosystem. All told, “more than 10,000 marine species each day hitch rides around the globe in the ballast water of cargo ships.” A number of *1013 these species are released into U.S. waters in the more than 21 billion gallons of ballast water released in the United States each year.

If these foreign organisms manage to survive and reproduce in the new ecosystem, they can cause severe problems in the natural and human environment. For example, zebra mussels, native to the Caspian Sea region of Asia, were brought into the Great Lakes in the ballast water of cargo ships. “Zebra mussels have clogged the water pipes of electric companies and other industries; infestations in the Midwest and Northeast have cost power plants and industrial facilities almost $70 million between 1989 and 1995.” As another example, according to a 2001 EPA report,

[a]n introduced strain of cholera bacteria, possibly released in the bilge water of a Chinese freighter, caused the deaths of 10,000 people in Latin America in 1991. This cholera strain was then imported into the United States from Latin America in the ballast tanks of ships that anchored in the port of Mobile, Alabama. Fortunately, cholera bacteria were detected in oyster and fínfísh samples in Mobile Bay ... and no additional deaths occurred from exposure to this pathogen.

With a lack of natural predators, invasive species can multiply rapidly and quickly take over an ecosystem, threatening native species. Indeed, invasive species “are a major or contributing cause of declines for almost half the endangered species in the United States.” Once established, invasive species become almost impossible to remove, leading “[sjcientists, industry officials, and land managers [to] recogniz[e] that invasive species are one of the most serious, yet least appreciated, environmental threats of the 21st century.”

In economic terms, invasive species can also have a devastating effect. The Department of Agriculture spends millions of dollars per year to detect and prevent invasive species. One study cited by the [General Accounting Office] concluded that “total annual economic losses and associated control costs [are] about $137 billion a year — more than double the annual economic damage caused by all natural disasters in the United States.”

Nw. Envtl. Advocates v. U.S. EPA (“Northwest Environmental Advocates II”), No. 03-05760, 2006 WL 2669042, at *3-4, 2006 U.S. Dist. LEXIS 69476, at *10-12 (N.D.Cal. Sept. 18, 2006) (citations omitted; sixth alteration added).

B. Procedural History

In January 1999, plaintiffs petitioned the EPA, asking that the agency repeal 40 C.F.R. § 122.3(a). See Petition for Repeal of 40 CFR § 122.3(a) (Jan.1999) (“Petition for Rulemaking”). Plaintiffs contended that the regulation was not authorized by the CWA and was thus ultra vires. Plaintiffs sued the EPA a year and a half later, alleging unreasonable delay in responding to their petition. The district court ordered the EPA to respond to the petition, but the EPA obtained a stay from this circuit. Under a subsequent consent decree, the EPA agreed to “grant, deny, or grant in part and deny any remaining part of NWEA’s petition” by September 2, 2003. Nw. Envtl. Advocates v. U.S. EPA, 340 F.3d 853, 857 (9th Cir.2003). On the day of the deadline, the EPA denied plaintiffs’ petition in its entirety. See EPA, Decision on Petition for Rulemaking To Repeal 40 C.F.R. 122.3(a) (Sept. 2, 2003) (“EPA Decision on Petition”); see also Availability of Decision on Petition for Rulemaking To Repeal Regulation Related to Ballast Water, 68 Fed.Reg. 53,165 (Sept. 9, 2003) (giving notice of the denial).

*1014 Plaintiffs brought suit against the EPA three months later, in December 2003. Their first cause of action alleged that 40 C.F.R. § 122.3(a) is not authorized by the CWA and is thus ultra vires. See 5 U.S.C. § 706(2)(C). Their second cause of action alleged, based on their ultra vires argument, that the 2003 EPA Decision on Petition was “not in accordance with law.” See 5 U.S.C. § 706(2)(A). At the same time, as a protective measure in the event that the district court lacked jurisdiction, the plaintiffs filed directly with this court a petition for review of the EPA Decision on Petition, pursuant to jurisdictional provisions contained in 33 U.S.C. § 1369(b)(1).

In March 2005, the district court granted summary judgment to plaintiffs on their first cause of action and ordered the EPA to repeal § 122.3(a). Nw. Envtl. Advocates v. U.S. EPA (“Northwest Environmental Advocates I”), No. 03-05760, 2005 WL 756614, at *7, 2005 U.S. Dist. LEXIS 5373, at *40 (N.D.Cal. Mar. 30, 2005). It is unclear whether the district court reached plaintiffs’ second cause of action. Given the court’s holding on the plaintiffs’ first cause of action, however, it did not need to do so. The district court ordered further proceedings to determine the appropriate remedy. Id. The six states intervened as plaintiffs at the remedy stage “to protect their sovereign, proprietary, regulatory, and economic interest in the States’ waters.” The Shipping Industry Ballast Water Coalition (“Shipping Coalition”) intervened as a defendant. In September 2006, the district court vacated the challenged portions of 40 C.F.R. § 122.3(a) as of September 30, 2008. Nw. Envtl. Advocates II, 2006 WL 2669042, at *1, 2006 U.S. Dist. LEXIS 69476, at *2.

The EPA and the Shipping Coalition (collectively, “the EPA”) appealed the district court’s decision to this court. We consolidated their appeal with the petition filed directly in this court.

II. Standard of Review

We review de novo questions of subject matter jurisdiction, Ecology Ctr., Inc. v. U.S. Forest Serv., 192 F.3d 922, 924 (9th Cir.1999); the legal question of whether a statute of limitations applies, Sierra Club v. Penfold, 857 F.2d 1307, 1315 (9th Cir.1988) (as amended); a district court’s grant of summary judgment, Envtl. Prot. Info. Ctr. v. U.S. Forest Serv., 451 F.3d 1005, 1008 (9th Cir.2006); and the legal question of whether a plaintiff has exhausted the necessary administrative remedies, Great Basin Mine Watch v. Hankins, 456 F.3d 955, 961 (9th Cir.2006).

Under 5 U.S.C. § 706(2)(C), the provision we apply to the plaintiffs’ first cause of action, we must “set aside agency action” that is “in excess of statutory jurisdiction, authority, or limitations, or short of statutory right.” This standard requires the application of Chevron U.S.A., Inc. v. Natural Resources Defense Council, 467 U.S. 837, 104 S.Ct. 2778, 81 L.Ed.2d 694 (1984). See, e.g., Nat’l Mining Ass’n v. Fowler, 324 F.3d 752, 758 (D.C.Cir.2003); Anna Jacques Hosp. v. Leavitt, 537 F.Supp.2d 24, 29-30 (D.D.C.2008) (“To determine if the Secretary exceeded his statutory authority in violation of 5 U.S.C. § 706(2)(C), the Court must engage in the two-step inquiry required by Chevron.”).

When “reviewing an agency’s statutory interpretation under the APA’s ‘not in accordance with lav/ standard,” see 5 U.S.C. § 706(2)(A), the standard applied to the plaintiffs’ second cause of action, we also “adhere to the familiar two-step test of Chevron.” Holland v. Nat’l Mining Ass’n, 309 F.3d 808, 815 (D.C.Cir.2002); cf. Cleveland v. Ohio, 508 F.3d 827, 838 (6th Cir.2007) (“Agency action is ‘not in accordance with the law1 when it is in conflict with the language of the statute.... ”).

*1015 We review the district court’s remedial order for abuse of discretion. Biological Legal Found, v. Badgley, 309 F.3d 1166, 1176 (9th Cir.2002).

III. Discussion

The EPA argues that the district court lacked subject matter jurisdiction over plaintiffs’ suit, and that we therefore have subject matter jurisdiction over the appeal only insofar as necessary to order the district court to dismiss the suit for want of jurisdiction. On the alternative assumption that the district court had subject matter jurisdiction, the EPA argues that the statute of limitations bars the ultra vires claim contained in the plaintiffs’ first cause of action; that the district court erred on the merits in finding that the CWA did not authorize the exemptions contained in 40 C.F.R. § 122.3(a); and that the district court abused its discretion in choosing its remedy.

A. Subject Matter Jurisdiction

The district court had subject matter jurisdiction over plaintiffs’ suit under the general federal question statute, 28 U.S.C. § 1331, unless some other statute divested the district court of jurisdiction. The only statute that could have had that effect is section 509(b)(1) of the CWA. See 33 U.S.C. § 1369(b)(1). Section 509(b)(1) specifies seven categories of agency action for which a challenge must be brought as an original proceeding in a court of appeals rather than in a district court. The EPA contends that plaintiffs’ ultra vires challenge to § 122.3(a) falls within two of these seven categories. If the EPA is right as to either category, the district court did not have subject matter jurisdiction, and we must review the EPA’s action by means of plaintiffs’ petition for review filed directly in this court.

We do not lightly hold that we have jurisdiction under section 509(b)(1). We have “counseled against [its] expansive application.” League of Wilderness Defenders/Blue Mountains Biodiversity Project v. Forsgren, 309 F.3d 1181, 1190 n. 8 (9th Cir.2002). “The specificity and precision of section [509], and the sense of it, persuade us that it is designed to exclude” EPA actions that Congress did not specify. Longview Fibre Co. v. Rasmussen, 980 F.2d 1307, 1313 (9th Cir.1992). Indeed, “[n]o sensible person ... would speak” with such detail otherwise. Id.

We address the two potentially relevant categories of section 509(b)(1) in turn, concluding that the agency action falls in neither category. The district court therefore had subject matter jurisdiction over plaintiffs’ suit.

1. Section 509(b)(1)(E)

Subsection 509(b)(1)(E) provides for review by a court of appeals of EPA actions “in approving or promulgating any effluent limitation or other limitation under section 1311, 1312, 1316, or 1345 of this title.” See 33 U.S.C. § 1369(b)(1)(E) (referring to sections 301, 302, 306, and 405 of the CWA). The CWA defines an “effluent limitation” as “any restriction ... on quantities, rates, and concentrations of chemical, physical, biological, and other constituents which are discharged from point sources....” 33 U.S.C. § 1362(11); see also 40 C.F.R. § 122.2 (same); cf. 33 U.S.C. §§ 1311, 1314(b) (establishing a procedure for adopting effluent limitations guidelines).

Section 509(b)(1)(E) authorizes original court of appeals jurisdiction for challenges to regulations that establish numerical limitations and similar limits. For example, in Natural Resources Defense Council v. U.S. EPA, 673 F.2d 400, 402 (D.C.Cir.1982) (“NRDC D.C.Cir.”), the D.C. Circuit exercised jurisdiction under section 509(b)(1)(E) over a challenge to regulations setting forth “a complex set of procedures for issuing or denying NPDES per *1016 mits.” In upholding its jurisdiction, the D.C. Circuit characterized the regulations as “restriet[ing] who may take advantage of certain provisions or otherwise guid[ing] the setting of numerical limitations in permits,” and as constituting “ ‘a limitation on point sources and permit issuers’ and ‘a restriction on the untrammeled discretion of the industry’ that existed before passage of the CWA.” Id. at 404-05 (quoting Va. Elec. & Power Co. v. Costle, 566 F.2d 446, 450 (4th Cir.1977)).

The regulation in this case can be characterized as “approving or promulgating any effluent limitation or other limitation” only if those words are understood in a Pickwickian sense. The regulations in NRDC D.C.Cir. established procedures under which limitations on discharges of effluent would be implemented. Unlike the regulations in that case, 40 C.F.R. § 122.3(a) provides no limitation whatsoever.

We conclude that section 509(b)(1)(E) does not authorize original jurisdiction in the court of appeals in this case. Section 122.3(a) does not involve the approval or promulgation of “any effluent limitation or other limitation,” but rather creates the categorical and permanent exemptions of three types of discharges from any limit imposed by a permitting requirement.

2. Section 509(b)(1)(F)

Section 509(b)(1)(F) provides for review by a court of appeals of EPA actions “in issuing or denying any permit under section 1342 of this title.” See 33 U.S.C. § 1369(b)(1)(F) (referring to section 402 of the CWA).

In Crown Simpson Pulp Co. v. Costle, 445 U.S. 193, 196, 100 S.Ct. 1093, 63 L.Ed.2d 312 (1980), the Supreme Court held that section 509(b)(1)(F) also covers EPA actions “functionally similar” to the denial of permits. The facts of the case make clear that the Court understood functional similarity in a narrow sense. The State of California, which had been delegated permit granting authority under the CWA, proposed granting point source permits to pulp mills discharging pollutants into the ocean. See id. at 194-95, 100 S.Ct. 1093. If California had not been delegated permit granting authority, the EPA would have granted or denied the permits directly. See id. at 196-97, 100 S.Ct. 1093. The EPA vetoed the proposed permits. See id. at 194, 100 S.Ct. 1093. Because the EPA was not the permit-granting entity, the plaintiff contended that the EPA’s action was not the issuance or denial of a permit within the meaning of section 509(b)(1)(F). See id. at 195, 100 S.Ct. 1093. The Court concluded instead that the fortuitous circumstance that this case arose in a state with permit-granting authority should not produce a different jurisdictional result from a case involving a state without such authority. Id. at 196— 97, 100 S.Ct. 1093; see also Ga.-Pac. Corp. v. U.S. EPA, 671 F.2d 1235, 1238-40 (9th Cir.1982) (exercising original jurisdiction over denial of a variance); Pac. Legal Found, v. Costle, 586 F.2d 650, 655 (9th Cir.1978) (exercising original jurisdiction over extension of a permit), rev’d on other grounds, 445 U.S. 198, 100 S.Ct. 1095, 63 L.Ed.2d 329 (1980).

In American Mining Congress v. U.S. EPA 965 F.2d 759, 763 (9th Cir.1992), we exercised jurisdiction under section 509(b)(1)(F) over a challenge to an EPA regulation of stormwater discharges from inactive mining operations. The EPA concluded that these discharges required permits because they were “associated with industrial activity” under section 402(p)(2)(B) of the CWA. The challenged regulation therefore required permits for most inactive mines, but, based on temporary permitting delays provided by section 402(p), the regulation exempted “reclaimed” inactive coal mines from the per *1017 mit requirement until the expiration of a moratorium. Id. The Mining Congress, representing inactive mines required to obtain permits, challenged the portion of the regulation requiring permits. Id. at 764. The Mining Congress used the exemption of reclaimed mines to argue that other inactive mines should receive the same favorable treatment. Id. at 764-65. American Mining Congress is inapplicable to our case because the Mining Congress challenged the requirement that certain mines obtain a permit, not an exemption.

We have applied section 509(b)(1)(F) in two cases involving challenges to stormwa-ter regulations where those regulations were based in part on exemptions specified in the text of the CWA. In Natural Resources Defense Council v. U.S. EPA (“NRDC 9th Cir.1992”), 966 F.2d 1292 (9th Cir.1992), we exercised jurisdiction under section 509(b)(1)(F) over a challenge to a complex set of regulations governing discharges from stormwater runoff. See id. at 1296-97. Two statutory provisions formed the basis for the regulations. First, as mentioned above, section 402(p) of the CWA, 33 U.S.C. § 1342(p), “established deadlines by which certain storm water dischargers must apply for permits, the EPA or states must act on permits and dischargers must implement their permits.” NRDC 9th Cir.1992, 966 F.2d at 1296. This section required that particularly important categories of discharges be regulated quickly, and exempted less important categories of discharges from regulation until 1992. Id. at 1295-96; see also Envtl. Def. Ctr., Inc. v. U.S. EPA 344 F.3d 832, 840, 843 (9th Cir.2003) (exercising jurisdiction over challenge to stormwa-ter discharge regulations promulgated under section 402(p)). Second, CWA section 402(Z)(2), 33 U.S.C. § 1342(i)(2), exempted certain stormwater discharges by mining, oil, and gas facilities from CWA permitting requirements. See NRDC 9th Cir.1992, 966 F.2d at 1306-07. The Natural Resources Defense Council argued that the EPA had extended the deadline for storm sewer discharges beyond the dates authorized by CWA section 402(p); that the EPA had defined improperly what constituted certain kinds of storm sewer discharges, so that some discharges were exempted from permitting requirements for a longer period than section 402(p) allowed; and that the EPA had erred in defining what constituted stormwater discharges from mining, oil, and gas facilities, improperly expanding the exemption from the permitting requirement contained in section 402(Z)(2). NRDC 9th Cir.1992, 966 F.2d at 1299-1309.

In Natural Resources Defense Council v. U.S. EPA (“NRDC 9th Cir.2008 ”), 526 F.3d 591 (9th Cir.2008), we exercised jurisdiction under section 509(b)(1)(F) over a challenge to a regulation exempting certain stormwater discharges from mining, oil, and gas facilities. Id. at 601. Two CWA provisions lay behind the regulation. First, section 402(i)(2), mentioned above, exempted discharges from mining, oil, and gas facilities. Second, an amendment to the CWA specified that the exemption contained in section 402(i)(2) included discharges from construction activities at mining, oil, and gas facilities. See Energy Policy Act of 2005, Pub.L. No. 109-58, § 323, 119 Stat. 594, 694; 33 U.S.C. § 1362(24) (codifying the amendment to section 502). The Natural Resources Defense Council challenged the regulation as exempting a broader category of discharges than permitted under CWA sections 402(Z)(2) and 502. NRDC 9th Cir.2008, 526 F.3d at 600-01.

In both of these cases in which we exercised jurisdiction under section 509(b)(1)(F), statutory provisions explicitly provided the underlying exemptions. The challenged regulations sought to define more precisely those discharges that came *1018 within statutory exemptions (and thus did not need permits) and those that did not come within statutory exemptions (and thus needed permits). In contrast, the case now before us challenges a regulation providing exemptions not contained in section 402 or in any other section of the CWA. This case thus does not involve the “issuing or denying[of] any permit under Section 402.” See Natural Res. Def. Council v. Train, 396 F.Supp. 1393, 1402 (D.D.C.1975), aff'd, sub nom. Natural Res. Def. Council v. Costle, 568 F.2d 1369 (D.C.Cir.1977).

We conclude by agreeing with the district court’s analysis in a suit very similar to the one before us. In Environmental Protection Information Center v. Pacific Lumber Co., 266 F.Supp.2d 1101, 1108-09 (N.D.Cal.2003), the court addressed an EPA regulation that permanently exempted an entire class of silvicultural discharges from any NPDES permitting requirement. The district court noted that the court of appeals in NRDC D.C.Cir. had upheld original jurisdiction under section 509(b)(1) on the ground that if there were no such jurisdiction, there would be a “‘perverse situation’ in which the court ‘will be able to review the grant or denial of the permit, but will be without authority to review directly the regulations on which the permit is based.’ ” Id. at 1114 (quoting Natural Resources Defense Council, Inc. v. U.S. EPA (“NRDC D.C.Cir.”), 656 F.2d 768, 775 (D.C.Cir.1981)). The district court wrote:

Because [plaintiff] challenges a decision that in effect excludes sources from the NPDES program, the circuit courts will never have to confront the issuance or denial of a permit for these sources. The Ninth Circuit, by virtue [of the regulation], will never have to consider on direct review an action involving the denial of an NPDES permit for pollutant discharges [within the exemption provided by the regulation]. Thus, a district court taking jurisdiction over a challenge to the silvicultural regulation does not create the same awkwardness for a circuit court as that described in [NRDC D.C.Cir.].

Id. at 1115-16 (footnote omitted) (upholding its own jurisdiction under 28 U.S.C. § 1331).

We conclude that § 509(b)(1)(F) does not authorize original jurisdiction in the court of appeals in this case. Section 122.3(a) does not involve the issuance or the denial of a permit or a functionally similar action, but rather the permanent exemptions of three types of discharges from any permitting requirement.

B. Statute of Limitations

The applicable statute of limitations provides that “every civil action commenced against the United States shall be barred unless the complaint is filed within six years after the right of action first accrues.” See 28 U.S.C. § 2401(a). The EPA promulgated the final version of 40 C.F.R. § 122.3(a) in 1979. The EPA denied plaintiffs’ Petition for Rulemaking in September 2003. Plaintiffs filed suit in December 2003. Whether their first cause of action is barred by the statute of limitations depends on whether their right of action first accrued in the 1970s when the EPA promulgated the regulation or in 2003 when the EPA denied plaintiffs’ petition. The EPA conceded in the district court and in its brief to this court that the statute of limitations does not bar plaintiffs’ second cause of action. See Nw. Envtl. Advocates I, 2005 WL 756614, at *7, 2005 U.S. Dist. LEXIS 5373, at *22.

Our decision in Wind River Mining Corp. v. United States, 946 F.2d 710 (9th Cir.1991), controls our analysis. In Wind River, the Bureau of Land Management (“BLM”) had classified certain federal lands as Wilderness Study Areas *1019 (“WSAs”) in 1979. Mining was forbidden in a WSA. Id. at 711. In 1986 and 1987, the Wind River Mining Corporation asked the BLM to declare that its decision to create a WSA was invalid.