Natural Resources Defense Council v. National Marine Fisheries Service (71 F. Supp. 3d 35, 2014)

MEMORANDUM OPINION

KETANJI BROWN JACKSON, United States District Judge

The federal government has been gravely concerned about the depletion of fish in the waterways off the coast of the United States as a result of fishing activity since at least the mid-1970s, when Congress enacted the Magnuson-Stevens Fishery Conservation and Management Act. Pub.L. No. 94-265, 90 Stat. 352 (1976) (codified as amended at 16 U.S.C. § 1801 et- seq. (2012)). The Magnuson-Stevens Act seeks to “promote domestic commercial and recreational fishing” while employing “sound conservation and management principles” in order to ensure “the optimum yield from each fishery.” Id. § 1801(b)(3) — (4). The instant case arises from an attempt'by the National Marine Fisheries Service (“NMFS”) to pursue the twin aims of the Magnuson-Stevens Act in relation to the specMed hind and the war-saw grouper — two species of fish that live in the deep waters of the Atlantic Ocean and that are especially vulnerable to being “subjected to a level of fishing mortality” that threatens the capacity of each stock to replenish its population levels. 50 C.F.R. § 600.310(e)(2)(i)(B) (describing this phenomenon and labeling it “overfishing”).

In December of 2010, the NMFS promulgated a regulation that banned outright the catching and retention of speckled hind and Warsaw grouper, which had been listed as undergoing overfishing since 1997. In addition, because scientific research suggested that these particular stocks of fish would nevertheless continue to be endangered as a result of their accidental or incidental catch when fishermen in the region targeted other deep water species (a circumstance known as “by-catch”), the NMFS also prohibited the targeting of six other species of fish that the NMFS then believed “co-occurred” (i.e., lived) with the speckled hind and the war-saw grouper in certain deep water areas of the South Atlantic Snapper-Grouper Fishery. In May of 2012, the NMFS reconsidered its co-occurrence findings and reversed course, enacting Regulatory Amendment 11, which lifted the prohibition related to the targeting of the six other deep water stocks. Plaintiffs Natural Resources Defense Council and Ocean Conservancy (“Plaintiffs”) — nonprofit environmental protection organizations' that strenuously object to the NMFS’s change in policy — have filed this action against the NMFS, the National Oceanic and Atmospheric Administration (“NOAA”), the Department of Commerce, and the Secretary of the Department of Commerce (collectively, “Defendants”) to challenge Regulatory Amendment 11 on the grounds that it violates the Administrative Procedure Act (“APA”), 5 U.S.C. § 500 et seq., as well as the Magnuson-Stevens Act itself.

Before this Court at present are the parties’ cross motions for summary judgment. Plaintiffs assert that the undisputed administrative record establishes that the NMFS lifted the six-stock deep water prohibition largely due to pressure from fishing communities that stood to profit greatly if fishing for the six other species was permitted once again; thus, according to Plaintiffs, Regulatory Amendment 11 was arbitrary and improper. Defendants maintain that, although economic considerations did factor into the agency’s decision, NMFS’s primary reason for lifting the prohibition was its reasonable and well-supported determination that because the six stocks of fish do not, in fact, co-occur with speckled hind and Warsaw grouper, the six-stock deep water prohibition was an ineffective conservation measure.

On September 3Ó, 2014, this Court issued an Order announcing that Plaintiffs’ motion for summary judgment is DENIED and Defendants’ cross-motion for summary judgment is GRANTED. (Order, ECF No. 46.) In the instant Memorandum Opinion, the Court explains the reasoning behind that ruling. In short, after reviewing the record and the parties’ submissions and hearing oral argument on the motions, this Court has determined that the NMFS adopted Regulatory Amendment 11 based on a reasonable analysis of the available data and that the agency sufficiently explained its change in policy. Moreover, it is clear to this Court that the NMFS’s conclusion that the 'six-stock deep water prohibition should be repealed is not inconsistent with the tenets of the Magnuson-Stevens Act.

I. BACKGROUND

Plaintiffs’ challenge to Regulatory Amendment 11 arises out of the “complicated statutory and regulatory system governing [] federal fisheries.” Lovgren v. Locke, 701 F.3d 5, 13 (1st Cir.2012). A brief description of the federal -fishery management scheme is warranted, because a basic understanding of the applicable laws and regulations — and, in particular, how such federal restrictions on fishing activity are developed and adopted — -is necessary for full comprehension of the NMFS action that is being challenged here.

A. The Federal Fishery Management System

Congress enacted the Magnuson-Ste-vens Act in 1976 to address the combination of increased fishing activity in certain coastal areas (known as “fishing pressure”), habitat losses, and inadequate conservation and management practices that threatened the survival of certain stocks of fish. See 16 U.S.C. § 1801(a)(2). When it amended the Magnuson-Stevens Act in 2006, Congress reiterated its intent to continue to “conserve and manage [U.S.] fishery resources,” and to “promote domestic commercial and recreational fishing under sound conservation and management principles.” Id. § 1801(b)(1) — (3); see also NRDC v. Nat’l Marine Fisheries Serv., 421 F.3d 872, 879 (9th Cir.2005) (“The Act sets this priority in part because the longer-term economic interests of fishing communities are aligned with the conservation goals set forth in the Act. Without immediate efforts at rebuilding depleted fisheries, the very long-term survival of those fishing communities is in doubt.”) (citations omitted).

To accomplish these goals, the Magnu-son-Stevens Act defined a federal fisheries conservation zone that extends between three nautical miles and two hundred nautical miles off the coast of the United States. Within this zone, federal authorities administer a fishing conservation and management program designed to prevent overfishing and to rebuild depleted stocks. This conservation and management program is developed through the cooperation of local, state, and federal government officials, and also other major stakeholders, including members of the commercial and recreational fishing industries and environmental and consumer organizations. Id. §§ 1801(b)(5); id. § 1852(b)(l)-(2). Because members of Congress tended to believe that “[t]he demise of the United States fisheries in the past is more accurately attributable to non management rather than to mis management,” the Mag-nuson-Stevens Act was specifically designed to offer the federal government “the tools for truly effective management” of the fishing activity in our nation’s coastal waters. Warren G. Magnuson, The Fishery Conservation and Management Act of 1976: First Step toward Improved Management of Marine Fisheries, 52 Wash. L.Rev. 427, 428 (1976-1977) (emphasis added).

Under the Magnuson-Stevens Act, Congress has designated the Secretary of Commerce as the manager of the fishery conservation and management program but in practice, the Secretary delegates his authority to the NMFS, which is a sub-agency of the NOAA within the Department of Commerce. See N.C. Fisheries Ass’n v. Gutierrez, 518 F.Supp.2d 62, 70-71 (D.D.C.2007); Flaherty v. Bryson, 850 F.Supp.2d 38, 43 n. 2 (D.D.C.2012); Fishermen’s Finest v. Locke, 593 F.3d 886, 889 (9th Cir.2010). In its role as the manager of the fisheries in America’s coastal waters, the NMFS has a number of tools at its disposal.

1. Regional Fishery Management Councils And Fishery Management Plans

The NMFS’s most important resource under the Magnuson-Stevens Act is eight “Regional Fishery Management Councils.” The Fishery Management Councils are boards that are meant to “reflect the expertise and interest of the several constituent States in the ocean area over which such Council is granted authority.” 16 U.S.C. at § 1852(a)(2). Accordingly, the Act requires the Secretary to appoint individuals to the Regional Fishery Management Councils who “by reason of their occupational or other experience, scientific expertise, or training, are knowledgeable regarding the conservation and management, or the commercial or recreational harvest, of the fishery resources of the geographical area concerned.” Id. § 1852(b)(2)(A). To meet the goal of broad-based participation by relevant stakeholders, the councils’ membership is drawn from the commercial and recreational fishing industries, and also environmental and consumer organizations, in addition to local, state, and federal officials. Id. §§ 1801(b)(5), 1852(b)(l)-(2).

The most significant responsibility of the Fishery Management Councils under the Magnuson-Stevens Act is the drafting of “Fishery Management Plans.” Id. § 1852(h)(1). Fishery Management Plans include data analyses and management measures for a fishery. Essentially they are recommendations to the Secretary of Commerce on the allocation of resources: the plans describe the environmental and economic status of the fishery and propose conservation and management measures that are “necessary and appropriate for the conservation and management of the fishery, to prevent overfishing and rebuild overfished stocks, and to protect, restore, and promote the long-term health and stability of the fishery.” Id. § 1853(a)(1)(A). “The ultimate goal [] of any [FJishery Management [P]lan is to establish measures which achieve a rate or level of fishing mortality that allows the fishery to produce the maximum sustainable yield on a continuing basis.” A.M.L. Int’l, Inc. v. Daley, 107 F.Supp.2d 90, 93 (D.Mass.2000) (citing 16 U.S.C. § 1802(29); 50 C.F.R. § 600.310(a)). In other words, Fishery Management Plans set the fishing activity rules for the fishery; if the fishery is overfished, the Fishery Management Plan will limit fishing in a way that allows the fishery to rebuild affected stocks of fish. See 16 U.S.C. § 1854(e)(2).

The Magnuson-Stevens Act mandates that the Regional Fishery Management Councils employ a variety of mechanisms to gather information when developing and updating Fishery Management Plans. Among other things, the Magnuson-Ste-vens Act instructs Fishery Management Councils to draw on the expertise of “Advisory Panels,” which are committees that are meant to represent all those people with a direct interest in the fishery, ranging from environmentalists, to sport fishermen, to members of the fishing industry. Id. §§ 1852(g)(2), 1852(g)(3)(B). Furthermore, under the Magnuson-Stevens Act, Fishery Management Councils are required to establish and maintain a Scientific and Statistical Committee (“SSC”) in order “to assist [the council] in the development, collection, evaluation, and peer review of such statistical, biological, economic, social, and other scientific information as is relevant to such Council’s development and amendment of any fishery management plan.” Id. § 1852(g)(1)(A). In addition to hearing from • these experts, Fishery Management Councils must also conduct public hearings “to allow all interested persons an opportunity to be heard in the development of fishery management plans and amendments to such plans, and with respect to the administration and implementation of the [Magnuson-Stevens Act].” Id. § 1852(h)(3).

2. The NMFS’s Rulemaking Process

Once a Fishery Management Council finishes drafting a proposed Fishery Management Plan in consultation with its expert and lay advisors, the Council submits the proposal to the NMFS. Id. § 1852(h)(i); Flaherty, 850 F.Supp.2d at 43. The NMFS, through the Secretary of Commerce, is responsible for the adoption and implementation of the Fishery Management Plans as well as any amendments to such plans. 16 U.S.C. § 1855(d) (“The Secretary shall have general responsibility to carry out any [Fishery [Management [P]lan or [A]mendment approved or prepared by him, in accordance with the provisions of this chapter.”). Upon receiving a Fishery Management Plan, the NMFS must “immediately” publish notice in the Federal Register soliciting comments on the Plan, see id. § 1854(a)(1)(B), and also must “immediately” review the Plan to determine whether it conforms to the standards set forth in the Magnuson-Stevens Act and any other applicable statute, see id. § 1854(a)(1)(A).

With respect to ensuring compliance with the Magnuson-Stevens Act’s standards, the NMFS generally determines whether a Fishery Management Plan includes conservation and management measures that are “necessary and appropriate ... to prevent overfishing and rebuild overfished stocks, and to protect, restore, and promote the long-term health and stability of the fishery.” Id. § 1853(a)(( )(A). Furthermore, the NMFS is tasked with the responsibility of verifying that the Fishery Management Plan satisfies the ten “national standards for fishery conservation and management” (hereinafter, “National Standards”) that the Magnuson-Stevens Act establishes. See id. § 1851(a). The National Standards mandate that Fishery Management Plans conform to certain enumerated ideals, including the following four principles:

(1) Conservation and management measures shall prevent overfishing while achieving, on a continuing basis, the optimum yield from each fishery for the United States fishing industry.

(2) Conservation and management shall be based upon the best scientific information available....

(8) Conservation and management measures shall, consistent with the conservation requirements of this chapter (including the preventing of overfishing and rebuilding of overfished stocks), take into account the importance of fishery resources to fishing communities ... in order to (A) provide for the sustained participation of such communities, and (B) to the extent practicable, minimize adverse economic impacts on such communities.

(9) Conservation and management measures shall, to the extent practicable, (A) minimize bycatch and (B) to the extent bycatch cannot be avoided, minimize the mortality of such bycatch.

Id.

Significantly for present purposes, National Standard Eight (quoted above) requires the NMFS to “focus on the welfare of fishing communities,” such that “where two alternatives in fact achieve similar conservation goals, the preferred option will be the alternative that provides the greater potential for sustained participation of fishing communities and that minimizes adverse economic impacts.” N.C. Fisheries Ass’n, 518 F.Supp.2d at 72, 92. However, National Standard Nine tempers the potentially negative impact on conservation efforts of considering the economic interests of the fishing community by addressing “bycatch” — i.e., the accidental or incidental catching of species that are “harvested in a fishery, but which are not sold or kept for personal use” 16 U.S.C. § 1802(2) — and specifically requires that Fishery Management Plans adopt measures that minimize bycatch “to the extent practicable.” Id. § 1851(a)(9).

Notably, although the Magnuson-Ste-vens Act’s National Standards do constitute statutory requirements upon which legal action can be based, “[t]he National Standards do not require any particular outcome with respect to allocations; rather, they provide a framework for the Council’s analysis.” Fishermen’s Finest, 593 F.3d at 896. Put another way, the National Standards are broadly worded statements of Congressional objectives for all fishery conservation and management measures, and the NMFS is “required [] to exercise discretion and judgment in balancing” these sometimes conflicting concerns. Alliance Against IFQs v. Brown, 84 F.3d 343, 350 (9th Cir.1996).

In addition to policing Fishery Management Plans for compliance with the National Standards, the NMFS is also responsible for enforcing other requirements of the Magnuson-Stevens Act with respect to certain specific provisions that, per the statute, must be included in Fishery Management Plans and Amendments. One such provision is particularly relevant to the instant dispute: it obliges all Fishery Management Plans and Amendments to specify “annual catch limits,” 50 C.F.R. § 600.310(b)(2)(iii), which are caps on the “level of annual catch of a [particular] stock or stock complex,” id. § 600.310(f)(2)(iv). An acceptable annual catch limit provision includes both (1) the permissible catch amount for each stock, and (2) “accountability measures” — a term óf art that refers to mechanisms for ensuring that the annual catch limit is not exceeded. 50 C.F.R. § 600.310(f)(2)(iv); id. § 600.3 10(g)(1). Catch limits and accountability measures are required in Fishery Management Plans in order to promote the “optimum yield” from a fishery; that is, the amount of fishing that will provide the “greatest overall benefit to the Nation, particularly with respect to food production and recreational opportunities, and taking into account the protection of marine ecosystems[.]” 16 U.S.C. § 1802(33)(A). As explained, the Council is required to include annual catch limits and accountability measures in their Fishery Management Plans, and it is the NMFS’s duty to ensure that such plans “implement ] regulations, or annual specifications, at a level such that overfishing does not occur in the fishery, including measures to ensure accountability.” Id. § 1853(a)(15).

During the NMFS’s review of any Fishery Management Plan for statutory compliance, the NMFS must “take into account the information, views, and comments received from interested persons.” Id. § 1854(a)(2)(A). Within thirty days of the end of the public comment period, the Secretary must “approve, disapprove, or partially approve” the Fishery Management Plan. 16 U.S.C. § 1854(a)(3). If the NMFS disapproves of the Plan, it must send a “written notice to the Council,” specifying “(A) the applicable law with which the plan or amendment is inconsistent; (B).the nature of such inconsistencies; and (C) recommendations concerning the actions that could be taken by the Council to conform such [P]lan or [Ajmendment to the requirements of applicable law.” Id. Conversely, if the NMFS approves of the Plan, the Magnu-son-Stevens Act directs the NMFS to implement the Plan through the promulgation of regulations consistent with the Plan. Id. § 1855(d). The Council may also propose and submit language for regulations implementing the Fishery Man-' agement Plan along with the Plan itself, in which case, the NMFS will review the proposed regulations for consistency with the Plan and publish those proposed regulations for notice-and-comment before promulgating final regulations. Id. § 1854(b)(1).

It is only after the NMFS promulgates regulations implementing a Fishery Management Plan that the Plan becomes binding on the fishery. That is, the Fishery Management Plans and Amendments that the Regional Fishery Management Councils prepare do not themselves carry the force of law and cannot be challenged until the NMFS enacts regulations to effectuate the proposals. See N.C. Fisheries Ass’n v. Gutierrez, 550 F.3d 16, 17 (D.C.Cir.2008). The actions of the NMFS in promulgating regulations to adopt a Fishery Management Plan are subject to judicial review under the APA. See id.

3. Amendments To Fishery Management Plans

“Once [a Fishery Management Plan] has been approved and implemented, continuing management of the subject fishery involves monitoring the fishery, evaluating new information, and adjusting the management program through changes to the [Fishery Management Plan] and/or to its implementing regulations.” See EPA, Office of Federal Activities, Final Guidance for Reviewing Environmental Impact Statements for Fishery Management Plans (“EPA Guidance Document”), TO-0008 for contract 68-W-03-029 (Sept. 2005), at 14. Fishery Management Plans themselves are amended through a process called “formal amendment,” while the regulations that implement such plans are altered through the “regulatory amendment” process.- Id. at 14, 17. Regulatory amendments “must follow normal rulemak-ing procedures,” but take less time to implement than Formal Amendments and are more easily modified. Id. at 17; see also N.C. Fisheries Ass’n, 518 F.Supp.2d at 73 (contrasting “plan amendments” with “more streamlined regulatory amendments”). Notably, “[a] regulatory amendment may [also] be used to implement a portion of an approved [Fishery Management. Plan] or Amendment that was reserved” by the NMFS at the time the Plan or Amendment was adopted. EPA Guidance Document at 17; see also id. (“A regulatory amendment offers considerable time savings over [a Formal] Amendment because future regulatory changes are anticipated within the scope of the [Fishery Management Plan].”).

The instant case involves both a formal amendment and a regulatory amendment to the South Atlantic Snapper-Grouper Fishery Management Plan.

B. The South Atlantic Snapper-Grouper Fishery

The South Atlantic Snapper-Grouper Fishery (the “Fishery”) is an area “off the coasts of North Carolina, South Carolina, Georgia, and Florida through the Atlantic side of Key West.” (S. Atl. Fishery Mgmt. Council, Regulatory Amendment 11 to the Management Plan for the Snapper Grouper Fishery of the South Atlantic Region (2011) (“RA 11”), AR Doc. 86 at 2958). Access to this Fishery “had been open and virtually unlimited prior to 1983,” but “conservation measures have vastly increased” during the last three decades, N.C. Fisheries Ass’n, 518 F.Supp.2d at 74; these measures have primarily been adopted and implemented under the Magnuson-Stevens Act, as described above, in the context of the South Atlantic Snapper-Grouper Fishery Management Plan.

Generally speaking, the primary aim of the various conservation restrictions that are in effect in this region is to protect and manage the sixty species of snapper and grouper that make up the Fishery, including eight “deep water” stocks relevant to this dispute: speckled hind, Warsaw grou-. per, blueline tilefish, snowy grouper, yel-lowedge grouper, misty grouper, queen snapper, and silk snapper. See Comprehensive Annual Catch Limit Am. for the South Atl., 77 Fed.Reg. 15,916 (Mar. 16, 2012). Although these eight stocks carry the deep water label, several of them can also be found in shallower waters. (RA 11, AR Doc. 86 at 2957, 2996.)

Commercial and recreational fisherman seek (i.e., “target”) each of these eight species in the Fishery to a different degree. The species that is targeted most— by far — is the blueline tilefish, followed by the snowy grouper. (Id. at 2980-82; Amendment 17B Final Rule, 75 Fed.Reg. 82,280 (Dec.30, 2010) (“17B Final Rule”), AR Doc. 5 at 45-46.) These two stocks often co-occur, meaning that they live in the same habitat within the Fishery and are typically found together. (17B Final Rule, AR Doc. 5 at 46; RA 11, AR Doc. 86 at 2957, 2967, 2996.) Yellowedge grouper, misty grouper, queen snapper, and silk snapper are not targeted at all, and these species are rarely encountered. (Mem. from Roy E. Crabtree, to Samuel D. Rauch III (Apr. 23, 2012) (“Apr. 2012 Crabtree Mem.”), AR Doc. 192 at 6100; Regulatory Amendment 11 Final Rule (“RA 11 Final Rule”),' 77 Fed.Reg. 27,374 (May 10, 2012), AR Doc. 196 at 6115; Final Appendices to Regulatory Amendment 11 (“Final App. to RA 11”), AR Doc. 87 at 3078; S. Atl. Fishery Mgmt. Council, Amendment 17B to the Fishery Management Plan for the Snapper-Grouper Fishery of the South Atlantic Region (2010) (“Am. 17B Envtl. Assessment”), 17B AR Doc. 195 at 14019-14020.)

The remaining two species — speckled hind and warsaw grouper — are the subject of the NMFS action being challenged in this case. Speckled hind and warsaw grouper are both large, deep water grouper species that dwell in reefs and rocky hard-bottom habitats along the South Atlantic seaboard. (RA 11, AR Doc. 86 at 2968-69.) Speckled hind can grow up to four feet long and can weigh over sixty-five pounds. (Id. at 2968.) Warsaw grouper are even larger than speckled hind; they can grow up to seven feet long and can weigh more than 500 pounds. (Id. at 2969.)

Because of certain aspects of their biology and their mating habits, both speckled hind and warsaw grouper are especially vulnerable to overfishing. First of all, both species are protogynous hermaphrodites, which means that they change sex from female to male as they grow and sexually mature. (17B Final Rule, AR Doc. 5 at 44; AR Doc. 86 at 2959.) Speckled hind are believed to reach sexual maturity after seven years, and can live as long as thirty-five years. (Gabriel L. Ziskin et at, Indications of Continued Overexploi-tation of Speckled Hind Along the Atl. Coast of the S.E. U.S., 140 Transactions of the Am. Fisheries Soc’y 384 (2011) (“Ziskin Study”), AR Doc. 16 at 294-95.) Warsaw grouper reach sexual maturity after approximately nine years and can live to be as much as forty-one years old. (Natural Res. Def. Council, Ocean Conservancy, and Pew Envtl. Grp., Comments on Request for Secretarial Disapproval of Regulatory Amendment 11 (Jan. 19, 2012) (“Comments on Request for Disapproval”), Ex. B, AR Doc. 203 at 6302.)

Second, speckled hind and warsaw grouper are “ontogenetic migrat[ing]” species, which means that they move from shallower to deeper water as they age. (S. Atl. Fishery Mgmt. Council, Snapper Grouper Comm., Summary Minutes (June 14-15, 2011) (“June 2011 Minutes”), • AR Doc. 48 at 1726; Final App. to RA 11, AR Doc. 87 at 3057-58.) According to the NMFS’s analysis of data regarding distribution and catch information, a significant population of both speckled hind and warsaw grouper has been observed in shallower waters. (March 23, 2012 Presentation Speckled Hind & Warsaw Grouper: A Review of Available Distribution and Catch Data (“March Presentation”), AR Doc. 127 at 4854-55.) However, the older fish are found in deeper waters; thus, deep water fishing disproportionately affects the grown, male fish, “reducing] spawning potential in the population.” (Ziskin Study, AR Doc. 16 at 894.) Deep water fishing also has the potential to harm large numbers of the grown male fish because speckled hind and Warsaw grouper spawn in groups, known as “spawning aggregations.” (RA 11, AR Doc. 86 at 2968.) This spawning aggregation behavior increases the likelihood that deep water fishermen may catch large groups of grown, male, breeding-capable fish faster than the stock can reproduce. (Id.; Comments on Request for Disapproval, AR Doc. 203 at 6302, 6320; Am. 17B Envtl. Assessment, 17B AR Doc. 195 at 13,890.)

Finally, some scientists maintain that speckled hind and Warsaw grouper experience “catastrophic decompression syndrome,” also known as “barotrauma,” a phenomenon in which the rapid change in pressure that occurs when a fish is dragged to the sea surface in a fishing net destroys the fish’s vital organs. (Ziskin Study, AR Doc. 16 at 298.) This means that, when these fish are caught in deeper waters — and, again, the speckled hind and Warsaw grouper in deeper waters are generally the adult, male, spawning members of the population — they are more likely to die as a result of being caught, even if they are immediately released. (Am. 17B Envtl. Assessment, 17B AR Doc. 195 at 14, 019.)

Perhaps due to their unique biological traits, both the speckled hind and the war-saw grouper have been subjected to overfishing in -the South-Atlantic Snapper-Grouper Fishery for nearly the past two decades. (See RA 11, AR Doc. 86 at 2959, 2993.) Scientists at the NMFS have studied the chronic overfishing problem with respect to these two species, and have found that, in addition to the obvious threat that is posed by direct targeting, a major unchecked source of the overfishing problem is incidental bycatch mortality. (See Ziskin Study, AR Doc. 16 at 294-95, 298; Ex. J. to Comments on Request for Disapproval, AR Doc. 203 at 6379, 6389.) That is to say, as of 2011, marine scientists have theorized that one reason for the observable decrease in the speckled hind and Warsaw grouper populations was the fact that groups of mature, male speckled hind and Warsaw grouper were, being accidentally caught during fishing trips that target co-occurring species, and were being killed as a result of barotrauma even if they were released back into the water. (See Ziskin Study, AR Doc. 16 at 298-99; see also Pis.’ Opp’n to Defs.’ Mot. for Summ. J. & Reply in Supp. of Pis.’ Mot. for Summ. J., ECF No. 36 (“Pis.’ Reply”) at 7 (summarizing the problem as the concern that “[bjycatch in deep water is more likely to kill [these] fish than in shallow water, and it alters the species’ male-female ratio and selectively kills the sexually mature members of the species.”).) As explained below, the NMFS recently took the lead in addressing this overfishing concern through its promulgation — and subsequent repeal — of various conservation measures.

C. Amendment 17B

In 2010, the South Atlantic Snapper-Grouper Fishery Management Council convened to consider the plight of the speckled hind and Warsaw grouper, and it ultimately proposed to the NMFS that the agency adopt Amendment 17B to the Snapper-Grouper Fishery Management Plan. Among other things, this formal amendment established an annual catch limit of zero for these two species. (Am. 17B Envtl. Assessment, 17B AR Doe. 195 at 14,018, 14,047.) Amendment 17B also implemented an accountability measure to ensure that the annual catch limit was met: it prohibited any and all harvest and possession of speckled hind or Warsaw grouper throughout the South Atlantic, meaning that fishermen could not retain and bring to shore even a single speckled hind or Warsaw grouper. (RA 11 Final Rule, AR Doc. 196 at 6115; Am. 17B Envtl. Assessment, 17B AR Doc. 195 at 14,018.) Despite these sweeping provisions, the Council concluded that prohibiting harvest and catch alone did not address the serious problem of bycatch mortality, and that other measures were needed to prevent overfishing. (17B Final Rule, AR Doc. 5 at 54 (noting that restrictions on landed catch alone “would not be sufficient'to end overfishing of speckled hind and Warsaw grouper due to discard mortality from fishing for other cooccurring deepwater species”); id. at 45 (noting that speckled hind and Warsaw grouper are long-lived and slow growing and require more stringent management measures, such as area closures, to end overfishing); RA 11, AR Doc. 86 at 2959; Am. 17B Envtl. Assessment, 17B AR Doc. 195 at 14,022.)

To address the bycatch problem, the Council included in Amendment 17B the contested provision at the heart of this dispute: a prohibition on the harvest and possession of six other snapper-grouper stocks in the fishery (blueline tilefish, snowy grouper, yellowedge grouper, misty grouper, queen snapper, and silk snapper) that were thought to co-occur with speckled hind and Warsaw grouper in depths of 240 feet or greater — the depth at which bycatch mortality of speckled hind and Warsaw grouper due to barotrauma was believed to be high. (Mem. from Roy E. Crabtree, Ph.D., to Eric C. Schwaab (Dec. 20, 2010) (“Dec. 2010 Crabtree Mem.”), 17B AR Doc. 228 at 14,477; 17B Final Rule, AR Doc. 5 at 43^4; RA 11, AR Doc. 86 at 2959.) Significantly, this six-stock deep water prohibition was not an complete closure of fishing waters, but instead was limited in two respects. First, the prohibition was limited to waters greater than 240 feet in depth; according to the Council, prohibiting harvest of co-occurring snapper-grouper species in such deep water “would provide protection to the largest, most fecund fish and ensure a natural sex ratio into the future.” (Am. 17B Envtl. Assessment, 17B AR Doc. 195 at 13,890.) Second, the prohibition was limited in scope: Amendment 17B only “[p]rohibit[ed] the harvest and possession of [the] species that are most often caught with speckled hind and Warsaw grouper in deeper waters[,]” leaving the same waters open to fishing that targeted other snapper-grouper stocks that were not believed to co-occur with these two species. (17B Final Rule, AR Doc. 5 at 44.) (emphasis added).

Although the Council eventually reached a consensus that the limited prohibition (referred to herein as “the six-stock deep water prohibition” or “the closure”) was the proper path, there was substantial internal opposition. The Council ultimately passed Amendment 17B at a December 2009 meeting with eight members in favor of the closure and five members dissenting. (See Mem. from Duane Hams to Dr. Roy Crabtree (Mar. 30, 2010) (“Harris Mem.”), 17B AR Doc. 193 at 13,829.) In March of 2010, the dissenting council members submitted a report outlining their opposition to the six-stock deep water prohibition (the “minority report”), which lodged two main challenges to the Council’s adoption of the Amendment 17B. (See Dec. 2010 Crabtree Mem., 17B AR-Doc. 228 at 14,478.) First, the minority report challenged the “assumption” that speckled hind and warsaw grouper co-occur with the six listed species in numbers that are substantial enough to warrant the prohibition. (Id. at 14,479.) In this regard, the minority report most fervently objected to the alleged association of these two species with blueline tilefish. (See id. at 14,478 (pointing to newly available information that suggested that blueline tilefish can be harvested without incidental by-catch of speckled hind and warsaw grouper); id. at 14,479 (noting that speckled hind and warsaw grouper co-occur more frequently with species not included in the prohibition).) Second, the minority report faulted the scientific basis for the six-stock deep water prohibition, contending that the majority had made an “inadequate assessment” of the data available regarding speckled hind and warsaw grouper, and that the available data itself was limited. (Id. at 14,478-79.)

After voting to approve Amendment 1713, including the controversial six-stock deep water prohibition, in December of 2009, the Council forwarded that Amendment to the NMFS for review and promulgation. (See Harris Mem., 17B AR Doc. 193 at 13,829.) Later that month, the NMFS promulgated a final rule implementing Amendment 1713, see 17B Final Rule, Amendment 1713, AR Doc. 5; 50 C.F.R. § 622; however, in recognition of the strong opposition from within the Council itself, the NMFS made clear that its “approval and impleméntation” of the six-stock deep water prohibition “does not preclude the Council from proposing future action to modify this prohibition if scientific information indicates it is appropriate to do so.” (1713 Final Rule, AR Doc. 5 at 46; see also id. (clarifying that “[r]e-addressing the deepwater closure will be accomplished through a regulatory amendment proposed by the Council at its December 2010 meeting”).)

D. Regulatory Amendment 11

At the same time as the NMFS was undertaking final action on Amendment 17B, the Council commenced its own reevaluation of the need for the six-stock deep water prohibition. As explained below, the Council’s reevaluation process primarily involved commissioning a study of existing data regarding where speckled hind and warsaw grouper are most frequently caught and with which species they co-occur — a study that is referred to in this opinion as “the Catch Analysis.” (Final App. to RA 11, AR Doc. 87 at 3041-43 (describing data sources).) This study prompted the Council to reverse its recommendation regarding the six-stock deep water prohibition and to propose that the NMFS adopt a regulatory amendment lifting that restriction. (See, e.g., June 2011 Minutes, AR Doc. 48 at 1736-42; S. Atl. Fishery Mgmt. Council, Snapper Grouper Comm., Summary Minutes (Aug. 9, 2011) (“Aug. 2011 Minutes”), AR Doc. 66 at 2287-91.) Thus, mere months after the NMFS promulgated the prohibition by enacting Amendment 17B, the NMFS was faced with the decision of whether or not to reverse itself and do away with that regulatory provision. The NMFS’s analysis of this question involved not only reviewing the Council’s recommendation and Catch Analysis, but also conducting its own additional research, preparing an environmental assessment of the impact of lifting the prohibition, considering public comment on the matter, and forming its own conclusions regarding the propriety of adopting Regulatory Amendment 11.

1. The Council Commissioned The “Catch Analysis” And Considered Alternatives .

The Council’s decision to recommend repealing the six-stock deep water prohibition was principally based on a study that scientists at the NMFS conducted at the Council’s request. The scientists assessed existing data regarding where speckled hind and warsaw grouper are, in fact, most frequently caught and with which species they co-occur. (Final App. to RA 11, AR Doc. 87 at 3041-58 (Catch Analysis).) The underlying data was collected during fishing trips from 1962 through 2010 (id. at 3041-43), and although this data was available prior to the implementation of Amendment 17B- and the deep water prohibition, the Council had not previously engaged in the type of detailed assessment that was done in the Catch Analysis. Specifically, the scientists conducted a “cluster analysis” óf observations of speckled hind and warsaw grouper, and homed in on data regarding where fisherman caught speckled hind and warsaw grouper when fishing for the other six stocks included in the prohibition. (M. at 3043.) The Catch Analysis showed that speckled hind and warsaw grouper are far more frequently found in shallow waters inshore of 240 feet (id. at 3048); however, it was acknowledged that this finding was due, in part, to the fact that most fishing occurs in shallower waters, so there is a much greater opportunity for the species to be observed in shallow areas. (Id. at 3046-47, 3056 (noting that the data “suffer[s] from biases for under-representation”).) Despite the higher frequency in shallow waters, the NOAA scientist who authored the Catch Analysis concluded that “the odds of encountering speckled hind and warsaw grouper are higher outside of 240 [feet].” (Id. at 3048 (emphasis added).) In other words, “[t]he highest odds of encounters for these species are in waters greater than 240 feet, although the data sources, in terms of absolute numbers, are much more inside of 240 feet.” (June 2011 Minutes, AR Doc. 48 at 1731.)

In addition to assessing the frequency and odds of encountering speckled hind and warsaw grouper, the Catch Analysis also assessed the probability of co-occurrence between those species and the other six stocks included in the deep water prohibition. (Final App. to RA 11, AR Doc. 87 at 3050-58.) The Catch Analysis indicated that speckled hind and warsaw grouper “rarely co-occurred” with any of the six stocks. (Id. at 3050.) In particular, the data indicated that blueline tilefish, snowy grouper, and yellowedge grouper were “distinctly separated from speckled hind and warsaw grouper.” (Id. at 3051.) Instead, speckled hind and warsaw grouper were more often found with stocks not included in the deep water prohibition. (Id. at 3050.) Zeroing in on the data behind blueline tilefish and snowy grouper, which are targeted most frequently in the fishery, the Catch Analysis attributed the low association of those species with speckled hind and warsaw grouper to habitat preferences: (1) whereas speckled hind and warsaw grouper prefer rocky hard-bottom habitats, blueline tilefish do not, and (2) snowy grouper are usually found in depths where speckled hind and warsaw grouper are not. (Final App. to RA 11, AR Doc. 87 at 3057.)

Significantly, when the Council reviewed' the Catch Analysis, it specifically recognized that the lower number of fishing trips in deep water meant that there was a more limited opportunity to ascertain the location of speckled hind and warsaw grouper at those depths and, more importantly, to test their co-occurrence with the other stocks in those waters. (See June 2011 Minutes, AR Doc. 48 at 1725-28, 1731-32 (repeatedly noting biases in the data).) Primarily because of this relative absence of information about fishing trips in the deep water area, there was some opposition to lifting the prohibition among members of the Council who believed that no protections should be removed without more information about speckled hind and warsaw grouper in the greater depths. (See, e.g., id. at 1725-28, 1731-32, 1738-40 (noting data limitations, expressing reservations about lifting the closure, and discussing alternatives).)

In an effort to balance the need for conservation measures to protect the speckled hind and warsaw grouper with the concern about being overly restrictive of fishing, the Council also considered nine alternatives to lifting the six-stock deep water prohibition in its entirety, including options that would have exempted either certain areas or certain species from the ban. (RA 11, AR Doc. 86 at 2989-3004.) But given the low co-occurrence that the Catch Analysis reflected, most Council members landed firmly on the decision to abolish the deep water prohibition altogether. (See, e.g., June 2011 Minutes, AR Doc. 48 at 1736 (Dr. Roy Crabtree, the NMFS’s Regional Administrator in the South Atlantic, noting that recent evidence “begs the question of what [ ] this deepwa-ter closure [is] really doing anymore”).) Ultimately, although various Council members recognized that some further protections would be needed, the Council unanimously voted to recommend elimination of the prohibition in its entirety, and to submit that proposal in the form of a regulatory amendment (Regulatory Amendment 11) to the NMFS for review and adoption. (Aug. 2011 Minutes, AR Doc. 66 at 2287-89 (roll call vote).)

2. The NMFS Conducted Additional Co-Occurrence Research

Presented with the Council’s recommendation to repeal the recently enacted six-stock deep water prohibition, the NMFS conducted additional research into co-occurrence of speckled hind and warsaw grouper with the other, stocks included in the prohibition, especially the potential co-occurrence of those species with blueline tilefish. In an unrelated confluence of events, the Council’s Science and Statistical Committee had proposed a twelve-fold increase in the total acceptable biological catch and optimal yield for blueline tilefish (Apr.2012 Crabtree Mem., AR Doc. 192 at 6099), which would mean that commercial fishermen could sustainably harvest much more blueline tilefish than in the past, and the NMFS was concerned that the optimal yield for blueline tilefish could not be achieved if the six-stock deep water prohibition remained in place. (Id. at 6119 (estimating annual economic loss to the blueline tilefish fishing community); RA 11 Final Rule, AR Doc. 196 at 6119 (noting that the deep water prohibition “would result in significantly greater economic losses to a segment of commercial snapper-grouper fisheries than originally anticipated when the Council approved Amendment 1TB.”).)

To further explore co-occurrence with blueline tilefish, the NMFS issued an exempted fishing permit (“EFP”) to a select group of fishermen, allowing them to target speckled hind and Warsaw grouper despite the existing prohibition. (RA 11, AR Doc. 86 at 2997, 3014; NMFS SERO presentation titled “Regulatory Amendment 11, Speckled Hind and Warsaw Grouper Catch Data” (June 14, 2011), AR Doc. 52 at 1977; see also generally Exempted Fishing Permit to Dr. Louis Daniel, on behalf of North Carolina Division of Marine Fisheries (Aug. 2, 2011) (“EFP”), AR Doc. 8 (letter granting and describing' EFP).) The NMFS limited the EFP to the deep water areas (defined as more than 240 feet deep) north of Cape Hatters, North Carolina (EFP, AR Doc. 8 at 67), and the North Carolina Division of Marine Fisheries monitored all fishing trips and assisted in data collection, eventually creating a report that compiled all of the EFP data (id. at 67-68).

The EFP data mirrored the results of the Catch Analysis: it found extremely low co-occurrence between speckled hind and Warsaw grouper with blueline tilefish. (See S. Atl. Fishery Mgmt. Council, Summ. Minutes (Mar. 8, 2012) (“Mar. 2012 Minutes”), AR Doc. 108 at 3783-86.) Of the 73 fishing trips made pursuant to the EFP in the deep water area off the North Carolina coast, fisherman caught 94,000 pounds of blueline tilefish but not a single speckled hind or Warsaw grouper. (Id. at 3784-3785 (“[W]ith this information here you can see that we are not seeing speckled hind and Warsaw grouper in this area, at these depths that are fished[.]”); see also Comments on Request for Disapproval, AR Doc. 203 at 6219 (noting the complete absence of deep water co-occurrence between speckled hind and Warsaw grouper); Mar. 2012 Minutes, AR Doc. 108 at 3786 (members of the Council noting that the EFP data was “pretty compelling”).)

3. The NMFS Prepared An Environmental Assessment

In addition to reviewing the Catch Analysis and commissioning the EFP data, the NMFS also prepared an Environmental Assessment to evaluate the environmental impact of an agency decision to lift the deep water prohibition. (RA 11, AR Doc. 86 at 2950-3040); cf. 42 U.S.C. § 4332. In the Environmental Assessment, which, among other things, evaluated the information presented in the Catch Analysis, the NMFS acknowledged uncertainty in the datasets used in the Catch Analysis (Final App. to RA 11, Appendix B, AR Doc. 87 at 3041-58 (noting various problems with the data)), but nonetheless found the data sufficient to show that “the probability of catching either [co-occurring] species with speckled hind and Warsaw grouper is low.” (RA 11, AR Doc. 86 at 2997.)

The NMFS also posited that, even though repealing the deep water prohibition “could result in the greatest level of negative biological effects as it would allow the greatest amount of fishing” overall, “with respect to speckled hind and Warsaw grouper” in particular, lifting the prohibition “could have the greatest positive biological effect for the species” because it could reduce fishing pressure and bycatch with respect to the shallower waters, where the species are most abundant, resulting in a smaller number of overall catch. (Id. (emphasis added).) In other words, based on the data in the Catch Analysis demonstrating that there are more speckled hind and Warsaw grouper in the shallower water than deeper water, the NMFS reasoned that the deep water prohibition might be leading fishermen to fish in shallower water than they otherwise would have, and by removing the deep water prohibition, those fishermen would move to deeper water, where there are fewer specked hind and Warsaw grouper to catch, so fewer speckled hind and Warsaw grouper would be caught overall. (See id. (noting that the Council’s SSC and Advisory Panel “indicated that the 240-foot (40 fathom closure) might actually increase fishing mortality of speckled hind and war-saw grouper if it resulted in a shift in fishing pressure [from the] deep water to the shelf edge (131 to 262 foot' depth) where speckled hind and Warsaw grouper are most abundant”).)

In addition, as part of the environmental review, the NMFS prepared its own “By-catch Practicability Analysis,” which evaluated the extent to which lifting the prohibition would affect bycatch of speckled hind and Warsaw grouper. (Final App. to RA 11, Appendix B, AR Doc. 87 at 3045-51.) In the Bycatch Practicability Analysis the NFMS again explained that eliminating the deep water prohibition “could reduce fishing pressure at the shelf-edge, which serves as a nursery area for speckled hind and Warsaw grouper. Therefore, positive biological effects could be expected for speckled hind and Warsaw through a reduction in the magnitude of bycatch[.]” (Id. at 3073, 3076).

Finally, the agency’s Environmental As- • sessment also evaluated the alternatives that the Council had considered and the expected outcome of each one. (See RA 11 (section titled “What Are the Biological Effects of the Proposed Alternatives on Protected Resources?”), AR Doc. 86 at 2996-3001.) With respect to the economic effect of each alternative'in particular, the NMFS concluded that, because the deep water prohibition was not actually serving any biological benefit, “any harvest reduction would be an unnecessary economic loss[,]” so lifting the deep water prohibition would have the most economic benefit. (Id. at 2999.) Furthermore, the NMFS provided an in-depth analysis of the expected social impact of each alternative on the fishing communities involved in the South Atlantic Snapper Grouper Fishery, which focused in large part on the alternatives that would allow fishermen to harvest blueline tilefish. (Id. at 2999-3002.)

4. The NMFS Considered Public Comment

On December 20, 2011, in light of the Catch Analysis, the EFP Data, and its own Environmental Assessment, the NMFS issued a proposed rule adopting Regulatory Amendment 11. (Regulatory Amendment 11 Proposed Rule, 76 Fed.Reg. 78,879 (Dec. 20, 20Í1) (“RA'll Proposed Rule”), AR Doc. 186 at 6082-84.) The NMFS’s proposal maintained that the six-stock deep water prohibition should be lifted because the measure was an ineffective means of protecting the speckled hind and warsaw grouper, given that (1) speckled hind and warsaw grouper are “rarely encountered” in the deep water areas that the prohibition covered; (2) speckled hind and warsaw grouper rarely co-occur with the species included in the prohibition; and (3) the prohibition imposed a greater than anticipated economic hardship on fishermen. (RA 11, AR Doc. 86 at 3006.) Thereafter, the NMFS solicited and considered public comments on Regulatory Amendment 11 and the proposed implementing regulations. (RA 11 Proposed Rule, AR Doc. 186; RA 11 Final Rule AR Doc. 196 at 6115-20.)

Plaintiffs submitted written comments that strenuously objected to NMFS’s proposed adoption of Regulatory Amendment 11 because, according to Plaintiffs, “it would remove a measure necessary to prevent overfishing of specked hind and War-saw grouper without providing an. adequate substitute.” (Pis.’ Mot. for Summ. J., ECF No. 32 (“Pis.’ Mot.”) at 22; AR Doe. 12 at 6263-80.) In their comments, Plaintiffs argued that “the Catch Analysis had concluded that these fish are more likely to occur in the deep water closure area than they are to occur in shallower waters, and that the closure was necessary to protect the mature, spawning individuals crucial to the species’ recovery.” (Pis.’ Mot. at 22.) Plaintiffs further stated that “the proposal would violate the Magnuson-Stevens Act by eliminating the only accountability measure covering bycatch of these species, and by failing to minimize bycatch and bycatch mortality to the extent practicable.” (Id.)

5. The Promulgation Of Regulatory Amendment 11

On May 10, 2012, following the notice and comment period for its Proposed Rule, the NMFS issued the final rule that repealed the six-stock deep water prohibition. (RA 11 Final Rule, AR Doc. 196 at 6120 (amending 50 C.F.R. § 622.35(o)).) The final rule underscored the NMFS’s conclusion that data analyzed or collected after Amendment 17B was passed (chiefly, the Catch Analysis, EFP Data, and' Environmental Assessment) had made clear that speckled hind and warsaw grouper did not actually co-occur with the six stocks included in the deep water prohibition. (See, e.g., id. at 6115-17 (referring the newly analyzed or newly available data).) Echoing its findings from the Environmental Assessment, the NMFS explained that, with respect to the blueline tilefish, the “low association ... may be attributable to the [species’] unique habitat preferences^]” and while other species earlier thought to have co-occurred with speckled hind and warsaw grouper may share similar habitat preferences, those other species were not targeted in the Fishery, and are rarely found with speckled hind and warsaw grouper in any event. (Id.) Moreover, the NMFS explained in the final rule that it had concluded that repeal of the six-stock deep water prohibition “would not likely result in significant increases in the bycatch mortality of speckled hind or warsaw grouper, although low levels of bycatch of these species might occur.” (Id. at 6117.)

The final rule also highlighted the fact that previously-implemented protection measures, including protected areas within the Fishery, seasonal closures, harvest and gear restrictions, and catch limits, still “are in effect even with the removal of the 240-ft [] prohibition^]” (Id. at 6117-19.) Finally, given the NMFS’s conclusion that the “prohibition is not an effective means to reduce discard mortality of speckled hind and warsaw grouper,” the final rule expounded on the economic consequences of keeping versus removing the deep water prohibition, which weighed in favor of removal. {Id. at 6114-6115 (noting that the closure was being lifted to “reduce the socio-economic impacts to fishermen harvesting deepwater snapper-grouper”); id. at 6119.) The NMFS noted, in particular, that it had considered, and rejected for various reasons, ten other alternatives to lifting the prohibition. {Id. at 6118.)

With the publication of the final rule on May 10, 2012, Regulatory Amendment 11 went into effect immediately. {Id. at 6119.)-

E. Procedural History

Nearly one month after the NMFS published the final rule implementing Regulatory Amendment 11, Plaintiffs filed the instant complaint in federal court. (Compl., ECF No. 1 (June 8, 2012).) Plaintiffs complaint contains three “causes of action” each of which alleges that Regulatory Amendment 11 is arbitrary and capricious and violates the Magnuson-Ste-vens Act in a particular way. Specifically, Plaintiffs maintain that the NMFS has unlawfully enacted a regulation that (1) fails to end overfishing .of the speckled hind and Warsaw grouper (see Compl. at ¶ 45-53 (first cause of action)); (2) fails to establish adequate annual catch limit mechanisms (see Compl. at ¶ 54-60 (second cause of action)); and (3) fails to minimize bycatch and bycatch mortality to the extent practicable (see Compl. at ¶ 61-67 (third cause of action)).

Defendants answered the complaint and filed the administrative record of Regulatory Amendment 11 on August 3, 2012. (Answer, ECF No. 22; Admin. R., ECF No. 23.) The parties later supplemented the administrative record to include certain materials from the administrative record of Amendment 17B, which they agreed were relevant to this dispute. (Defs.’ Suppl. to the Admin. R., ECF No. 39; see also Stip. & Order, ECF No. 31 (approving the parties’ agreement to supplement the administrative record to include materials from Amendment 17B).) Plaintiffs filed their motion for summary judgment on November 9, 20Í2 (Pis.’ Mot.); Defendants’ summary judgment motion followed on December 14, 2012 (Defs.’ Cross-Mot. for Summ. J. (“Defs.’ Mot.”), ECF No. 33.).

Plaintiffs’ motion for summary judgment includes two distinct sets of arguments. First, Plaintiffs argue that the undisputed administrative record demonstrates that Regulatory Amendment 11 failed to comply with the APA’s standards for rulemak-ing. {See Pis.’ Mot. at 26-42.) Second, Plaintiffs attack the substance of the final rule and its attendant regulations, contending that they violate the substantive prescriptions of the Magnuson-Stevens Act. {See id. at 42-54.) In their cross-motion, Defendants contend that the NMFS’s adoption of Regulatory Amendment 11 was- both procedurally and substantively proper. {See generally Defs.’ Mot.) The cross-motions were fully briefed as of February 8, 2013. {See Pis.’ Reply (filed Feb. 8, 2013).) On April 5, 2013, the matter was transferred to this Court. {See Minute Entry of Apr. 5, 2013.) ' A hearing on the parties’ eross-motions was held on July 30, 2013. (See Minute Entry of July 30, 2013.)

II. LEGAL STANDARDS

Summary judgment under Federal Rule of Civil Procedure 56(c) is normally appropriate when the pleadings and the record evidence demonstrate that “there is no genuine issue as to any material fact and that the moving party is entitled to judgment as a matter of law.” Fed. R. Civ. P. 56(a). However, that standard does not apply to cases involving review of a final agency action undertaken pursuant to the Magnuson-Stevens Act. Rather, “[t]he Administrative Procedure Act ... sets forth the full extent of judicial authority to review [such] executive agency action[,]” F.C.C. v. Fox Television Stations, Inc., 556 U.S. 502, 513, 129 S.Ct. 1800, 173 L.Ed.2d 738 (2009) (citations omitted); see also 16 U.S.C. § 1855(f)(1)(B) (reviewing court may set aside challenged agency action taken under Magnuson-Stevens Act based only on grounds specified in 5 U.S.C. § 706(2)); Ocean Conservancy v. Gutierrez, 394 F.Supp.2d 147, 155 (D.D.C.2005) (citations omitted) (“NMFS’s actions are reviewed by this Court in accordance with the judicial review provisions of the Administrative Procedure Act[.]”).

A reviewing court applying section 706 of the APA must “hold unlawful and set aside agency action, findings, and conclusions” that are “arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law.” 5 U.S.C. § 706(2); Motor Vehicle Mfrs. Ass’n v. State Farm Mut. Auto. Ins. Co., 463 U.S. 29, 34, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983). Generally speaking, an agency action is not arbitrary and capricious where the agency has “examine[d] the relevant data and articulate[d] a satisfactory explanation for its action including a rational connection between the facts found and the choice made.” State Farm, 463 U.S. at 43, 103 S.Ct. 2856 (internal quotation marks and citation omitted). Conversely, an agency rule is considered arbitrary and capricious if “the agency has relied on factors which Congress has not intended it to consider, entirely failed to consider an important aspect of the problem, offered an explanation for its decision that runs counter to the evidence before the agency, or is so implausible that it could not be ascribed to a difference in view of the product of agency expertise.” Id.; see also N.C. Fisheries Ass’n., 518 F.Supp.2d at 79.

Because “it is the role of the agency to resolve factual issues to arrive at a decision that is supported by the administrative record, [ ] the function of the district court is to determine whether or not as a matter of law the evidence in the administrative record permitted the agency to make the decision it did.” N.C. Fisheries Ass’n, 518 F.Supp.2d at 79 (internal quotation marks and citations omitted); see also id. (calling summary judgment in the APA context a “mechanism for deciding, as a matter, of law, whether the agency action is supported by the administrative record and otherwise consistent with the APA standard of review” (citing Richards v. INS, 554 F.2d 1173, 1177 n. 28 (D.C.Cir.1977))). Under this deferential standard, the court’s review is limited to the administrative record created by the agency, Camp v. Pitts, 411 U.S. 138, 142, 93 S.Ct. 1241, 36 L.Ed.2d 106 (1973); Holy Land Found. for Relief & Dev. v. Ashcroft, 333 F.3d 156, 160 (D.C.Cir.2003), and the agency’s decisions are entitled to a “presumption of regularity!,]” Citizens to Preserve Overton Park, Inc. v. Volpe, 401 U.S. 402, 415, 91 S.Ct. 814, 28 L.Ed.2d 136 (1971). Where there is room for disagreement, the court may not “substitute its judgment for that of the agency” and instead must only “consider whether the decision was based on a consideration of the relevant factors and whether there has been a clear error of judgment.” State Farm, 463 U.S. at 43, 103 S.Ct. 2856; see also Bloch v. Powell, 348 F.3d 1060, 1070 (D.C.Cir.2003).

Courts considering challenges to actions that an agency has taken pursuant to the Magnuson-Stevens Act owe an especially high degree of deference to the agency due to the “highly technical and scientific determinations” at issue