COLLEEN KOLLAR-KOTELLY, UNITED STATES DISTRICT JUDGE
Plaintiffs National Wildlife Federation and Minnesota Conservation Federation filed suit under the Administrative Procedure Act (“APA”), 5 U.S.C. § 701 et seq., against the United States Environmental Protection Agency challenging 40 C.F.R. § 124.55(b), which governs certain discharge permits issued by the EPA pursuant to the Clean Water Act. Presently before the Court is the Defendant’s  Motion to Dismiss for Lack of Jurisdiction. Upon consideration of the pleadings,  the relevant legal authorities, and the record as a whole, the Court finds it lacks jurisdiction over the Plaintiffs’ claim that section 124.55(b) is invalid. Accordingly, the Defendant’s motion is GRANTED and this case is DISMISSED.
A. Statutory Framework
The Clean Water Act (“CWA” or the “Act”) generally prohibits the discharge of pollutants except in compliance with the Act. 33 U.S.C. § 1311(a). One program that regulates permits for the discharge of pollutants is the National Pollutant Discharge Elimination System, or NPDES. Id. § 1342. A party seeking a discharge permit under the NPDES must obtain “a certification from the State in which the discharge originates or will originate . . . that any such discharge will comply with the applicable provisions [of the Clean Water Act].” Id. § 1341(a)(1). The certification must set forth
[A]ny effluent limitations and other limitations, and monitoring requirements necessary to assure that any applicant for a Federal  permit will comply with any applicable effluent limitations and other limitations, . . . standard of performance under section 1316 of this title, or prohibition, effluent standard, or pretreatment standard under section 1317 of this title, and with any other appropriate requirement of State law set forth in such certification, and shall become a condition on any Federal license or permit subject to the provisions of this section.
Id. § 1341(d); see generally 40 C.F.R. § 124.53. The EPA may not issue a permit until the state issues or waives the certification. Id.
The EPA may issue a general permit covering “one or more categories or subcategories of discharges . . . within a geographic area.” 40 C.F.R. § 122.28(a)(1). Before issuing the permit, the EPA publishes a draft permit, including the proposed conditions and monitoring requirements, in the Federal Register. Id. § 124.6(e). Following a notice and comment period and receipt of the relevant state certification(s) (or waiver thereof), the EPA issues the final permit. Id.; id. at §§ 124.15(a), 124.55(b). EPA regulations provide that, consistent with the “reasonable time” requirement of section 1341(a)(1), state certification must be granted or denied within sixty days. 40 C.F.R. § 124.53(c)(3), (d). If a state has not granted, denied, or waived certification by the time the draft VGP is prepared, the EPA sends a copy of the draft permit to the state and indicates that the state will be deemed to have waived its right to certify unless it does so within sixty days from the date the draft permit is mailed. Id. § 124.53(c)
“If there is a change in the State law or regulation upon which a certification is based, ” the state may issue a modified certification. 40 C.F.R. § 124.55(b). If the EPA receives the modified certification before the final permit issues, “the permit shall be consistent with the more stringent conditions which are based upon State law identified in such certification.” Id. However,
If the certification or notice of waiver is received after final agency action on the permit, the [EPA] may modify the permit on request of the permittee only to the extent necessary to delete any conditions based on a condition in a certification invalidated by a court of competent jurisdiction or by an appropriate State board or agency.
Id. (emphasis added). Section 124.55 was promulgated in 1980 as part of a comprehensive revision of the procedures governing the NPDES and other permitting systems. See 45 Fed. Reg. 33, 290 (May 19, 1980); Natural Res. Def. Council v. EPA, 673 F.2d 400, 401-02 & n.1 (D.C. Cir. 1980). The Complaint challenges the validity of the portion of section 124.55(b) that prohibits the EPA from modifying permits to include more stringent conditions added to a state certification after a final permit issues.
B. Vessel General Permit & Litigation History
Historically discharges incidental to the normal operation of a vessel were exempt from NPDES permitting requirements. See 45 Fed. Reg. 33418 (May 19, 1980) (promulgating 40 C.F.R. § 122.3). Judge Susan Illston of the United States District Court for the Northern District of California invalidated that exemption in March 2005, finding the regulation was in excess of the EPA’s authority under the Clean Water Act. Nw. Envtl. Advocates v. EPA, No. 03-5760, 2005 WL 756614, at *13 (N.D. Cal. Mar. 30, 2005). Effective December 19, 2008, discharges incidental to the normal operation of a vessel would be subject the permitting requirements of the Clean Water Act. 73 Fed. Reg. 79, 473 (Dec. 29, 2008).
On June 17, 2008, the EPA published draft NPDES general permits for discharges incidental to the normal operation of a vessel, applicable to discharges incidental to the normal operation of all recreational vessels and commercial vessels greater than or equal to 79 feet in length. 73 Fed. Reg. 34, 296 (June 17, 2008). The EPA requested a certification from the relevant state agencies, including the Minnesota Pollution Control Agency (“MPCA”), on July 8, 2008. Compl. ¶ 22. In response to MPCA’s draft certification, the Plaintiffs submitted comments contending that, among other things, the proposed certification would be insufficient to prevent invasive species from being introduced into Minnesota’s waters as a result of ballast water discharges ...