Conservation Council for Hawaii v. National Marine Fisheries Service

*1214AMENDED ORDER GRANTING CONSERVATION COUNCIL’S MOTION FOR SUMMARY JUDGMENT, GRANTING NRDC’S MOTION FOR SUMMARY JUDGMENT, DENYING NRDC’S MOTION FOR LEAVE TO SUBMIT EXTRA-RECORD EVIDENCE, AND GRANTING IN PART AND DENYING IN PART DEFENDANTS’ MOTION TO STRIKE

I. INTRODUCTION.

This case involves challenges by environmental groups to federal government actions affecting vast areas of the Pacific Ocean and the marine life in those areas. Before the court is a motion for summary judgment filed in Civil No. 13-00684 by Plaintiffs Conservation Council for Hawaii, Animal Welfare Institute, Center for Biological Diversity, and Ocean Mammal Institute (collectively, “Conservation Council”), and a separate motion for summary judgment filed in Civil No. 14-00153 by Plaintiffs Natural Resources Defense' Council, Inc., Cetacean Society International, Animal Legal Defense Fund, Pacific Environment and Resources Center, and Michael Stocker (collectively, “NRDC”). The cases were consolidated by stipulation, but the stipulation provided that separate summary judgment motions could be filed by the parties in each case. See ECF Nos. 22, 23, 24 (ECF Nos. cited in this order refer to the docket sheet in Civil No. 13-00684). The court grants both summary judgment motions.

The government actions that are challenged in this case permit the Navy to conduct training and testing exercises even if they end up harming a stunning number of marine mammals, some of which are endangered or threatened. Searching the administrative record’s reams of pages for some explanation as to why the Navy’s activities were authorized by the National Marine Fisheries Service (“NMFS”), this court feels like the sailor in Samuel Taylor Coleridge’s “The Rime of the Ancient Mariner” who, trapped for days on a ship becalmed in the middle of the ocean, laments, “Water, water, every where, Nor any drop to drink.”

II. FACTUAL BACKGROUND.

The issues in this case are best understood by examining specific details, but the court begins by providing a broad overview. This introductory section thus has the limited purpose of providing the context for the challenges raised by Conservation Council and NRDC to the actions taken by NMFS and the Navy. Illustrations will be provided in connection with the court’s analysis of specific challenges.

The Navy proposed to conduct training and testing activities in an area of the Pacific Ocean known as the Hawaii-Southern California Training and Testing (“HSTT”) Study Area. This area includes (1) the Southern California Range Complex, consisting of San Diego Bay and approximately 120,000 square nautical miles of ocean between Dana Point, California, and San Diego, California; (2) the Hawaii Range Complex, consisting of approximately 2.7 million square nautical miles of ocean around the Hawaiian Islands; (3) Silver Strand Training Complex, on and adjacent to the Silver Strand, an isthmus between San Diego Bay and the Pacific Ocean; (4) pierside locations in Hawaii and Southern California; and (5) a transit corridor between Southern California and Hawaii. See ECF No. 70, PagelD # 13556; ECF No. 79, PagelD #14041. Thirty-nine marine mammal species have been identified as occupying the HSTT Study Area, eight of which are endangered and one of which is threatened under the Endangered Species Act (“ESA”). See ECF No. 66-19, PagelD # 10214.

*1215In 2010, the Navy began the process of reviewing the environmental impact of its proposed activities and invited NMFS to act as a cooperating agency in the preparation of the environmental impact statement (“EIS”). The Navy ultimately issued its corrected Final Environmental Impact Statement (“FEIS”) on August 30, 2013, and NMFS adopted that FEIS on December 5, 2013. ECF No. 66-18, PagelD #10201; ECF 66-21, PagelD #10267. While working on the FEIS, the Navy was also consulting with NMFS on compliance with the Endangered Species Act and was applying for Letters of Authorization from NMFS under the Marine Mammal Protection Act (“MMPA”) that would allow the Navy to take, incidental to the Navy’s training and testing activities, a certain number of marine mammals in the HSTT Study Area.

Under the MMPA, “to take” means “to harass, hunt, capture, or kill, or attempt to harass, hunt, capture, or kill any marine mammal.” 16 U.S.C. § 1362(13). The Navy’s proposed activities included “[s]o-nar use, underwater detonations, airguns, pile driving and removal, and ship strike,” which the NMFS viewed as “the stressors most likely to result in impacts on marine mammals that could rise to the level of harassment, thus necessitating MMPA authorization.” ECF No. 66-19, PagelD # 10209.

The Navy sought authorization for the incidental take of the HSTT Study Area’s thirty-nine species of marine mammals by Level B harassment. Id. at PagelD # 10208. As applied to military readiness activities, Level B harassment is “any act that disturbs or is likely to disturb a marine mammal or marine mammal stock in the wild by causing disruption of natural behavioral patterns, including, but not limited to, migration, surfacing, nursing, breeding, feeding, or sheltering, to a point where such behavioral patterns are abandoned or significantly altered.” 16 U.S.C. § 1362(18)(B)(ii). In addition, the Navy sought authorization for the incidental take of twenty-four of the thirty-nine species of marine mammals by Level A harassment or mortality. ECF No. 66-19, PagelD # 10208. Level A harassment is “any act that injures or has the significant potential to injure a marine mammal or marine mammal stock in the wild.” 16 U.S.C. § 1362(18)(B)(i).

In December 2013, pursuant to the MMPA, NMFS issued its Final Rule applicable to the period from December 2013 through December 2018, and issued Letters of Authorization permitting the Navy to take marine mammals in the HSTT Study Area during that period. In summary, NMFS determined that the effect of the activities proposed by the Navy would have a “negligible impact” on all the marine mammal species and stocks that would be affected. See ECF No. 66-19, PagelD #10249. NMFS set authorized take levels for Level A and Level B harassment for each such species or stock. The authorized take levels were the levels requested in the Navy’s application and included authorized mortalities. See id. at PagelD # s 10244-48.

Also in December 2013, the NMFS-ESA Cooperation Division issued a final Biological Opinion concerning the Navy’s activities. The Biological Opinion included NMFS’s finding of “no jeopardy” to endangered whale species, authorization for an “unspecified numbér” of takes of turtles by vessel strikes, and a finding of “no jeopardy” to turtles.

Amended versions of the December 2013 LOAs and Biological Opinion subsequently issued. See ECF No. 67-22, PagelD # s 12766-69; ECF No. 67-23, PagelD #s 12784-87; ECF No. 67-19.

Conservation Council has sued NMFS, which falls under the jurisdiction of the *1216Department of Commerce, and other related parties, seeking judicial review under the Administrative Procedure Act (“APA”) of administrative decisions that Conservation Council asserts violate the National Environmental Policy Act (“NEPA”), the MMPA, and the ESA. See ECF No. 78. NRDC has sued NMFS and related federal officials as well as the Navy, similarly seeking judicial review under the APA for alleged violations of the MMPA and the ESA. See ECF No. 73. Plaintiffs in both cases seek summary judgment on all their claims.

For their part, Defendants contend that, having complied with the requirements of NEPA, the MMPA, and the ESA, they are entitled to summary judgment in their favor in both actions. See ECF No. 68; ECF No. 71.

III. STATUTORY FRAMEWORK.

This case requires analysis of four statu- • tory schemes.

A. MMPA.

The MMPA was enacted to address concern that “certain species and population stocks of marine mammals are, or may be, in danger of extinction or depletion as a result of man’s activities.” 16 U.S.C. § 1361(1). Congress noted that “such species and population stocks should not be permitted to diminish beyond the point at which they cease to be a significant functioning element in the ecosystem of which they are a part, and, consistent with this major objective, they should not be permitted to diminish below their optimum sustainable population.” 16 U.S.C. § 1361(2).

The MMPA imposes a general prohibition on the “taking” of marine mammals unless the taking falls under a statutory exception. See 16 U.S.C. § 1371(a).

One statutory exception to the prohibition on the taking of marine mammals permits “citizens of the United States who engage in a specified activity (other than commercial fishing) within a specified geographical region” to take “small numbers of marine mammals of a species or population stock” during “periods of not more than five consecutive years each” if the Secretary1 finds that “the total of such taking during each five-year (or less) period concerned will have a negligible impact on such species or stock and will not have an unmitigable adverse impact on the availability of such species or stock for taking for subsistence uses.” 16 U.S.C. § 1371(a)(5)(A)(i).

Congress amended the MMPA to exempt military readiness activities from the “specified geographical region” and “small numbers” requirements in 16 U.S.C. § 1371 (a) (5) (A) (i). See 16 U.S.C. § 1371(a)(5)(F). Therefore, take of marine mammals incidental to military readiness activities, such as the Navy’s activities at issue in this case, may be permitted if the taking will have a “negligible impact” on an affected species or stock and will not have “an unmitigable adverse impact on the availability of such species or stock for taking for subsistence uses.” 16 U.S.C. § 1371(a)(5)(A)(i).

If those two findings are made, the Secretary must prescribe regulations setting forth “permissible methods of taking” and *1217“other means of effecting the least practicable adverse impact on such species or stock and its habitat.” 16 U.S.C. § 1371 (a) (5) (A) (i) (I I) (aa). In determining the “least practicable adverse impact” with respect to a military readiness activity, the Secretary is required to consider “personnel safety, practicality of implementation, and impact on the effectiveness of the military readiness activity.” 16 U.S.C. § 1371 (a) (5) (A) (ii).

B. ESA.

The ESA requires federal agencies, in consultation with the Secretary of Commerce, to “insure that any action authorized, funded, or carried out by such agency ... is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species.” 16 U.S.C. § 1536(a)(2). “Jeopardize the continued existence of means to engage in an action that reasonably would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species.” 50 C.F.R. § 402.02.

The Secretary of Commerce has delegated responsibility for administering the ESA with respect to threatened and endangered marine species to NMFS. See 50 C.F.R. § 17.2; see also Trout Unlimited v. Lohn, 645 F.Supp.2d 929, 932 (D.Or.2007).

After completing consultation regarding a proposed action, NMFS must prepare a Biological Opinion that discusses whether the proposed action is likely to cause jeopardy and the effects of the proposed action on listed species or on the species’ critical habitat. 50 C.F.R. § 402.14(h). In preparing its Biological Opinion, NMFS must use “the best scientific and commercial data available.” 50 C.F.R. § 402.14(g)(8).

If NMFS concludes that a proposed action will result in the incidental taking of an endangered or threatened species but will not cause jeopardy, it must include in its Biological Opinion an “incidental take statement” specifying, among other things, “the impact of such incidental taking on the species” affected. See 16 U.S.C. § 1536(b)(4); 50 C.F.R. § 402.14®. If an endangered or threatened species of marine mammal is involved, the take must be authorized under the MMPA. See 16 U.S.C. § 1536(b)(4)(C). Under the ESA, a taking that complies with an incidental take statement “shall not be considered to be a prohibited taking of the species concerned.” See 16 U.S.C. § 1536(o )(2).

C. NEPA.

NEPA is the “basic national charter for protection of the environment.” 40 C.F.R. § 1500.1(a). Congress enacted NEPA to ensure that all federal agencies would factor environmental considerations into deci-sionmaking.

To achieve this goal, NEPA requires a federal agency to prepare an EIS for “major Federal actions significantly affecting the quality of the human environment.” 42 U.S.C. § 4332(2)(C). The EIS “shall provide full and fair discussion of significant environmental impacts and shall inform decisionmakers and the public of the reasonable alternatives which would avoid or minimize adverse impacts or enhance the quality of the human environment.” 40 C.F.R. § 1502.1.

An EIS shall “[rjigorously explore and objectively evaluate all reasonable alternatives, and for alternatives which were eliminated from detailed study, briefly discuss the reasons for their having been eliminated.” 40 C.F.R. § 1502.14(a). “[Substantial treatment” must be devoted “to each alternative considered in detail including the proposed action so that reviewers may *1218evaluate their comparative merits.” 40 C.F.R. § 1502.14(b). ' A “no action” alternative also must be considered. 40 C.F.R. § 1502.14(c).

In reviewing an EIS, courts must ensure that the agency has taken a “hard look” at the environmental consequences of the proposed action. See Earth Island Inst. v. U.S. Forest Serv., 351 F.3d 1291, 1300 (9th Cir.2003); Smallwood v. U.S. Army Corps of Eng’rs, Civ. No. 08-00512 DAE-KSC, 2009 WL 196228, at *10 (D.Haw. Jan. 26, 2009).

D. Administrative Procedure Act.

The APA is the vehicle through which challenges to agency action as viola-tive of the MMPA, ESA, and NEPA are brought to court. Oregon Natural Res. Council v. Allen, 476 F.3d 1031, 1036 (9th Cir.2007) (review of ESA challenge under the APA); Ocean Advocates v. U.S. Army Corps of Eng’rs, 402 F.3d 846, 858 (9th Cir.2005) (review of MMPA and NEPA challenges under the APA).

Under the APA, a court must set aside agency action that is “arbitrary” or “capricious.” 5 U.S.C. § 706; see also Butte Envtl. Council v. U.S. Army Corps of Eng’rs, 620 F.3d 936, 945 (9th Cir.2010). Review under the arbitrary and capricious standard is “highly deferential, presuming the agency action to be valid and affirming the agency action if a reasonable basis exists for its decision.” Sacora v. Thomas, 628 F.3d 1059, 1068 (9th Cir.2010) (internal quotation marks omitted). “A reasonable basis exists where the agency considered the relevant factors and articulated a rational connection between the facts found and the choices made.” Arrington v. Daniels, 516 F.3d 1106, 1112 (9th Cir.2008) (internal quotation marks omitted). An agency’s decision will be set aside only if

it has relied on factors which Congress had not intended it to consider, entirely failed to consider an important aspect of the problem, offered an explanation for its decision that runs counter to the evidence before the agency, or is so implausible that it could not be ascribed to a difference in view or the product of agency expertise.

Butte, 620 F.3d at 945 (internal quotation marks omitted). A court may not “infer an agency’s reasoning from mere silence.” Crickon v. Thomas, 579 F.3d 978, 982 (9th Cir.2009) (internal quotation marks omitted). “[E]ven when an agency explains its decision with less than ideal clarity, a reviewing court will not upset the decision on that account if the agency’s path may reasonably be discerned.” Id.

IV. LEGAL STANDARD.

The parties ask this court to resolve their dispute through summary judgment motions. Summary judgment shall be granted when “the movant shows that there is no genuine dispute as to any material fact and the movant is entitled to judgment as a matter of law.” Fed. R.Civ.P. 56(a) (2010); see Addisu v. Fred Meyer, Inc., 198 F.3d 1130, 1134 (9th Cir.2000). However, in the context of reviewing an administrative decision under the APA, “there are no disputed facts that the district court must resolve.” Occidental Eng’g Co. v. I.N.S., 753 F.2d 766, 769 (9th Cir.1985). “[T]he 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.” Id.; see also City & Cnty. of San Francisco v. United States, 130 F.3d 873, 877 (9th Cir.1997). “[S]ummary judgment is an appropriate mechanism for deciding the legal question of whether the agency could reasonably *1219have found the facts as it did.” Occidental, 753 F.2d at 770.

V. EXTRA-RECORD MATERIAL.

A. NRDC’s Motion for Leave to Submit Extra-Record Evidence is Denied.

Judicial review of agency action is generally limited to the administrative record. Lands Council v. Powell, 395 F.3d 1019, 1029 (9th Cir.2005). There are narrow exceptions to this general rule. Extra-record evidence may be allowed when “(1) supplementation is necessary to determine if the agency has considered all factors and explained its decision; (2) the agency relied on documents not in the record; (3) supplementation is needed to explain technical terms or complex subjects; or (4) plaintiffs have shown bad faith on the part of the agency.” San Luis & Delta-Mendota Water Auth. v. Jewell, 747 F.3d 581, 603 (9th Cir.2014) (quoting Fence Creek Cattle Co. v. U.S. Forest Serv., 602 F.3d 1125, 1131 (9th Cir.2010)). NRDC relies on the third exception, arguing that extra-record evidence is necessary to clarify complex scientific concepts for the court. See ECF No. 76, PagelD # 13857.

The court does not agree with NRDC that it needs the extra-record evidence NRDC wishes to submit. The exceptions to the general rule against extra-record evidence “operate to identify and plug holes in the administrative record.” Powell, 395 F.3d 1019, 1030 (9th Cir.2005). NRDC fails to identify any holes in the administrative record that need to be plugged. Many of the terms and concepts NRDC identifies as warranting explanation are adequately explained in the record or need not be reviewed in such depth that additional evidence is needed.

B. Defendants’ Motion to Strike is Granted in Part and Denied in Part.

Defendants move to strike the Declaration of Robin W. Baird, Ph.D., and Exhibits 1, 3, 4, and 5 to the declaration, arguing that no exception to the general rule barring extra-record evidence applies. See ECF No. 53, PagelD # 1993.

Conservation Council argues that the Baird declaration is necessary to explain complex scientific matters and to show whether NMFS considered all factors and explained its decision. See ECF No. 83, PagelD # s 14268-74. Exhibit 1 is Baird’s curriculum vitae. Conservation Council also argues that Exhibits 3, 4, and 5 may be taken into account to show whether NMFS considered all factors and explained its decision. See id. at PagelD # s 14257-67.

The court strikes the Baird declaration and Exhibit 1. Conservation Council fails to show that the Baird declaration is necessary to explain technical terms or complex subjects. Conservation Council does not point to any specific concepts or terms absent from, or inadequately addressed in, the administrative record. While Conservation Council contends that the Baird declaration “provides necessary technical expertise” regarding the scientific tools available to NMFS, ECF No. 83, PagelD # 14270, Conservation Council does not show that such “technical expertise” is needed to decide the motions before this court. Conservation Council may be offering the Baird declaration to explain the material contained in Exhibits 3, 4, and 5, but it is not clear that those documents require further explanation.

Nor is the Baird declaration necessary to a determination as to whether NMFS considered all factors and explained its decision. Exhibits 3, 4, and 5 respond to that need on their own, and no scientific interpreter is necessary.

*1220The court will supplement the administrative record with Exhibits 3, 4, and 5. Those documents are offered to show the existence of particular factors, approaches, or analyses that NMFS did not utilize. This is a purpose falling squarely within the first exception to the general rule barring extra-record evidence. See Jewell, 747 F.3d at 603 (extra-record evidence is permitted if: “(1) supplementation is necessary to determine if the agency has considered all factors and explained its decision” (quoting Fence Creek Cattle Co. v. U.S. Forest Serv., 602 F.3d 1125, 1131 (9th Cir.2010))). As Conservation Council notes, it must be able to show the existence and availability of a particular approach to support its argument that the approach was relevant and was not considered by NMFS. See Asarco, Inc. v. U.S. Envtl. Prot. Agency, 616 F.2d 1153, 1160 (9th Cir.1980) (“It will often be impossible ... for the court to determine whether the agency took into consideration all relevant factors unless it looks outside the record to determine what matters the agency should have considered but did not. The court cannot adequately discharge its duty to engage in a ‘substantial inquiry’ if it is required to take the agency’s word that it considered all relevant matters.”).

Exhibits 3, 4, and 5 were all prepared by NMFS, are all publicly available and easily accessible, and present no facts new to the parties, unlike the declarations submitted by NRDC, which provide new explanations or interpretations of matters in the administrative record.

The Baird declaration (ECF No. 79-1) and any references to it are stricken. Exhibit 1, Dr. Baird’s curriculum vitae (ECF No. 79-2), is stricken as irrelevant. The court has not considered any of the stricken material in arriving at its summary judgment rulings.

VI. CONSERVATION COUNCIL AND NRDC ARE ENTITLED TO SUMMARY JUDGMENT.

A. NMFS’s “Negligible Impact” Finding Under the MMPA is Arbitrary and Capricious.

To permit the taking of marine mammals incident to military readiness activities, NMFS is required to find that the taking will have a “negligible impact” on affected species or stock. 16 U.S.C. § 1371(a)(5)(A)(i). Under the MMPA, a taking has a “negligible impact” if it “cannot be reasonably expected to, and is not reasonably likely to, adversely affect the species or stock through effects on annual rates of recruitment or survival.” 50 C.F.R. § 216.103.

While NMFS has found that the Navy’s proposed activities will have a “negligible impact” on affected species or stock in the HSTT Study Area, that finding is so insufficiently supported as to be arbitrary and capricious.

1. NMFS Must Examine the Impact of the Authorized Take, Not the Anticipated Take.

Before analyzing the bases NMFS provides for its “negligible impact” finding, this court resolves an unexpected dispute. The parties have spilled much ink over the subject of what kind of take needs to have only a negligible impact. Conservation Council and NRDC are adamant that the take that NMFS has authorized must have - a negligible impact. See ECF No. 89, PagelD #14357; ECF No. 90, PagelD # 14368. Defendants, however, say that what is relevant in this case is the take that is anticipated. In Defendants’ view, NMFS is “required to find that the incidental take expected from the activity, not the take requested, would have a negligible impact on affected species.” ECF No. 88, PagelD # 14338.

*1221In this case, the take requested was the take authorized, and the take authorized exceeds what NMFS and the Navy say is the take that is anticipated. In short, this threshold determination is not merely technical; there are substantial differences between the anticipated take numbers and the authorized take numbers. For example, the Navy is authorized to kill nineteen small odontocetes (e.g., dolphins) and pin-nipeds (e.g., seals, sea lions) per year by testing activities using impulsive sound sources, even though the Navy says it expects no such mortalities to occur. See ECF No. 66-6, PagelD # 9558. The Navy is also authorized to kill six large whales per year by vessel strike, even though the Navy says that the likelihood of such mor-talities is virtually nil. See id. at PagelD # 9636.

This dispute takes the court by surprise for two reasons. First, the MMPA makes it clear that it is authorized take that must be evaluated in determining whether there will be only a negligible impact. Specifically, the MMPA says that the Secretary “shall allow ... the incidental ... taking .... of ... marine mammals of a species or population stock if the Secretary ... finds that the total of such taking ... will have a negligible impact on such species or stock.” 16 U.S.C. § 1371(a)(5)(A)© (emphasis added). Because “the total of such taking” is the incidental taking that the Secretary “shall allow,” this court concludes that the statute looks to the authorized take.

Second, if an agency bases its finding on the anticipated take but can then authorize a far greater take than is anticipated, the authorized take could end up having no basis at all. Suppose, for example, that the Navy anticipated that a particular exercise would kill one sperm whale in a certain stock of that endangered species, and NMFS found that to be a negligible impact. Under Defendants’ reasoning, NMFS could then authorize the killing of any number of sperm whales, just because only one killing was anticipated. It makes no sense for NMFS to be able to authorize ten, fifty, or a hundred killings once it finds that the anticipated killing of one whale will have a “negligible impact.” The impact of taking the additional nine, forty-nine, or ninety-nine whales would not have been considered at all before being authorized.

In fact, allowing any agency to apply this kind of reasoning to authorize the taking of marine mammals could not only mean authorizing the wiping out of endangered and threatened species, it could also mean authorizing the extinction of even marine mammals that are not endangered or threatened. After all, under Defendants’ reasoning, if the taking of a hundred mammals was anticipated and an agency found that for that particular plentiful mammal the loss of a hundred would have a negligible impact, Defendants’ reasoning would allow the agency to authorize the taking of a million such mammals.

While the court doubts that Defendants would argue that the MMPA allows the exaggerated example the court posits, and the court is certainly not suggesting that Defendants have any interest in giving or receiving authorization for such a take, that example is precisely where Defendants’ argument leads.

This court’s focus throughout this case will be on the take authorized by NMFS. As a practical matter, it is the exceeding of the authorized take level that triggers a review .of the Navy’s activities by NMFS. See 54 Fed.Reg. at 40,347 (Sept. 29, 1989) (“[W]hen an incidental take authorization is exceeded, the activity must be reevaluated.”). While a review may also occur if the anticipated take is exceeded, even defense counsel conceded at the hearing on these motions that a review is not neces*1222sarily required solely because the anticipated take level is exceeded. Indeed, as defense counsel noted at the hearing, the very reason that the Navy sought authorization of takes in excess of anticipated levels in the first place was that the Navy wanted to avoid having its exercises interrupted. If it had Letters of Authorization providing authorized take levels, the Navy would not need to stop its activities even if the activities were clearly affecting marine mammals, so long as the Navy did not exceed the authorized take levels. The Navy thus considered the authorized take to be a check on its behavior, while nothing in the record suggests that the anticipated take operated with equivalent effect.

No one is disputing the importance of military readiness, but recognition of that importance does not permit the parties or this court to ignore the MMPA. Although MMPA provisions have been adjusted with respect to military activities, those adjustments do not permit the Navy to skirt the MMPA purely to avoid having its training and testing activities interrupted. Focusing on the authorized take, this court therefore turns to the bases of NMFS’s “negligible impact” finding to determine whether that finding is supportable.

2. NMFS Failed To Analyze the Effects of Authorized Takes on Many Affected Species and Stocks.

The MMPA requires examination of the impact of the activities in issue not only on affected species, but also on affected stocks of marine mammals. A “stock” refers to a group of marine mammals within a species, spch as the Island of Oahu’s stock of bottlenose dolphins, or the California coastal stock of bottlenose dolphins. See 16 U.S.C. § 1362(11) (“The term ‘population stock’ or ‘stock’ means a group of marine mammals of the same species or smaller taxa in a common spatial arrangement, that interbreed when mature.”).

Conservation Council and NRDC contend that NMFS’s “negligible impact” finding is arbitrary and capricious because NMFS failed to address the effects of authorized take on all the marine mammal species and stocks affected. This court agrees.

The requirement that NMFS examine the effect on every species and stock affected is contained in the statutory provisions permitting the taking of marine mammals of a species or population stock upon a finding that the authorized taking “will have a negligible impact on such species or stock and will not have an unmitiga-ble adverse impact on the availability of such species or stock for subsistence uses.” 16 U.S.C. § 1371 (a)(5)(A)(i) (emphasis added). Notwithstanding this statutory requirement, the court is unable to locate in the voluminous administrative record a discussion of all the affected species and stocks.

NMFS did prepare a “Five-Year Regulation” or Final Rule, and that document does contain a section with the heading “Species-Specific Analysis.” ECF No. 66-19, PagelD # s 10249-52. However, despite its promising heading, that section overlooks numerous species and stocks.

The “Species-Specific Analysis” includes a subsection on “mysticetes” that mentions “humpback, blue, Western North Pacific gray, fin, and sei whales” without including a separate discussion of the effects on the population of each. There is a discussion of humpback whale activity around Hawaii and the Navy’s agreement to limit its activities in the designated Humpback Whale Cautionary Area. There is also a reference to the use of waters in the Southern California portion of the HSTT Study Area as a summer feeding ground by the California, Oregon, Washington stock of humpback whales. This cursory reference by no means corresponds to a review of the *1223effect of the Navy’s activities on that stock. The report also says that feeding areas for fin and blue whales overlap the SOCAL Range Complex but asserts that major training events are not typically planned there and that the whales are large enough to be easily avoided.

Without analyzing the content of each subsection within the “Species-Specific Analysis” section, the court notes that the subsections cover sperm whales, pygmy and dwarf sperm whales, Dali’s porpoise, beaked whales, false killer whales, short-beaked common dolphins, California sea lions, northern fur seals, northern elephant seals, and Hawaiian monk seals. Conservation Council complains that NMFS never discusses stocks of Guadalupe fur and harbor seals; bottlenose, Fraser’s, long-beaked common, northern right whale, Pacific white-sided, pantropical spotted, Ris-so’s, rough-toothed, spinner, and striped dolphins; and killer, pygmy killer, short-finned pilot, and melonheaded whales. ECF No. 78, PagelD # 14004.

Defendants point to two pages of NMFS’s Final Rule preceding the “Species-Specific Analysis,” see ECF No. 66-19, PagelD # s 10248-49, but those pages do not explain NMFS’s determination that authorized take would’ have a negligible impact on the species and stock not mentioned in the “Species-Specific Analysis.” Defendants also cite to. large portions of NMFS’s Proposed Rule, but many of the pages cited are irrelevant to the present inquiry. The pages that bear some relevance discuss the potential effects of impulsive and nonimpulsive sound sources and vessel strike on marine mammals, but do not examine, with specific reference to the Navy’s proposed activities, what impact those potential effects may have on annual rates of recruitment and survival of affected species and stock. See ECF No. 66-10, PagelD # s 9902-16.

This court is not saying that an agency may never group stocks in considering the effects of a proposed activity. The court can certainly envision the possibility that, if a certain species typically reacts to a certain stimulus in a certain manner, an agency may have a basis for assuming that members in different stocks of that species will react similarly. That is, if, for example, a certain species of whale typically leaves an area when sonar signals are emitted at a certain distance, level, and volume, there may be no reason for an agency to have to discuss reactions stock-by-stock. That does not mean, however, that the analysis of population effects may be grouped, as it is unlikely that different stocks of the same species will share the same population numbers, or have identical sex, age, and reproduction statistics such that the effects of ar^activity on the different stock populations can be assumed to be identical.

The clearest evidence that NMFS failed to consider the impact of the Navy’s activities on all the affected species and stocks is ironically contained in the chart it submitted in response to an order requiring that Defendants provide specific record references by species and stock to show that NMFS did indeed consider the effect of the Navy’s activities on all affected species and stocks. See ECF No. 95.- With respect to the stocks not addressed in NMFS’s “Species-Specific Analysis,” NMFS provides record references to only general discussions with little, if any, relevance to the population-level effects on specific species and stock, and to concluso-ry statements that no such effects are expected. This is nothing short of an admission that many stocks and species lack discussions in the record about the effects of the proposed Navy activities on them specifically. See, e.g., ECF No. 95-1, Pa-gelD # s 14543-53 (citing exactly the same 10 pages in the administrative record for *122425 stocks, including stocks from different species, with frequent direction for the reader looking at the chart entry for one stock to see the chart entry for another stock).

The chart is particularly notable for highlighting how little attention NMFS gave to the effect on the populations of affected species and stocks of the mortalities the Navy was asking NMFS to authorize. In the chart, NMFS cites to brief discussions in the administrative record of mortalities of short-beaked common dolphins, Northern elephant seals, and California sea lions by explosion, stating for each that lethal takes “would be unlikely to have measurable long-term consequences” because the stock consists of hundreds of thousands of animals. See ECF No. 64-22, PagelD # s 5684, 5686, 5694, 5695; see also id. at, PagelD # s 5698, 5704. For the remaining species and stocks affected by lethal takes, NMFS cited to no analysis at all of the population-level effects of lethal takes.

That NMFS cannot point to where it analyzed the impact of at least deaths on all species and stocks is particularly troubling to the court. The court can no more find the rationale for NMFS’s conclusion that “any mortalities that do occur up to the maximum authorized levels would have a negligible impact on marine mammal species or stocks,” ECF No. 68 at PagelD # 13500, than it can find the rationale for NMFS’s almost identical statement that “any resulting impacts to individuals are not expected to affect annual rates of recruitment or survival,” ECF No. 66-19, PagelD # 10250. The most Defendants do is cite pages of NMFS’s Final Rule, ECF No. 66-19, PagelD #s 10248-49, that are silent with respect to numerous species and stocks. Thus, the court cannot determine from the pages Defendants cite why NMFS concluded, for example, that the fifteen large whale mortalities authorized will have a negligible impact on the whale species affected. This failure is especially puzzling in light of NMFS’s recognition that “[t]he death of a female of any of the large whale species would result in a reduced reproductive capacity of the population or species.” ECF No. 67-19, Pa-gelD # 12661.

NMFS must “articulate[ ] a rational connection between the facts found and the choices made.” Arrington, 516 F.3d at 1112 (internal quotation marks omitted). While not concluding that the discussions of the species and stocks mentioned in the “Species-Specific Analysis” are adequate, the court has no hesitation in saying that, when NMFS does not actually analyze the impact on certain species and stocks, NMFS does not satisfy its burden of showing how it reached its conclusions with respect to those species and stocks. The court is left unable to determine how NMFS could conclude what impact the Navy’s activities would have on the recruitment or survival of those species and stocks.

For species and stocks that are at least mentioned, this court sees no reason to examine whether NMFS sufficiently considered the impact of the proposed Navy activities on them. That is because it is not clear that the Navy would even have applied for authorization to take only those species and stocks. The Navy knew that its proposed activities would likely affect more than those species and stocks, and authorization to take fewer than all affected species and stocks would not likely have sufficed for the Navy’s purposes.

NMFS’s failure to explain the bases of its conclusion with respect to all species and stocks affected renders its “negligible impact” findings arbitrary and capricious. See Ctr. For Biological Diversity v. Kempthorne, 588 F.3d 701, 710 (9th Cir.2009) (“A negligible impact finding is arbitrary and capricious under the MMPA ... *1225if the agency ... entirely failed to consider an important aspect of the problem.” (internal quotation marks omitted)).

The court understands that NMFS may not have readily available data for each stock. Even if, as NMFS argues, it has no duty to create such data, it can hardly justify concluding that the Navy’s activities will have only a “negligible impact” on every stock, much less justify setting stock-specific authorized take levels, if it has no information on which to base such a conclusion or authorized take level. That is clearly arbitrary and capricious. Having made “negligible impact” findings and set authorized take levels for all affected species and stocks without articulating its bases, NMFS acted arbitrarily and capriciously.

3. NMFS Failed to Use the “Best Scientific Evidence Available.”

Under 50 C.F.R. § 216.102(a), NMFS was required to use the “best scientific evidence available” in making its finding of “negligible impact.” NMFS acted arbitrarily and capriciously in failing to use the best scientific evidence available.

Conservation Council and NRDC point to more than one kind of scientific evidence that they complain NMFS should have relied on but ignored. In this order, this court zeroes in on one particular kind of evidence that NMFS disregarded: evidence of “Potential Biological Removal” (“PBR”) levels. A PBR level is defined in the MMPA as “the maximum number of animals, not including natural mortalities, that may be removed from a marine mammal stock wile allowing that stock to reach or maintain its optimum sustainable population.” 16 U.S.C. § 1362(20); see ECF No. 78, PagelD # s 14007-08. NMFS authorized the Navy to kill marine mammals in 15 stocks at levels much higher than their PBR levels. Because any mortality level that exceeds PBR will not allow the stock to reach or maintain its optimum sustainable population (“OSP”), such a mortality level could not be said to have only a “negligible impact” on the stock.

Indeed, the MMPA provides that “species and population stocks ... should not be permitted to diminish below their optimum sustainable population.” 16 U.S.C. § 1361(2). See also 54 Fed.Reg. at 40,341, 40,342 (“In order to make a negligible impact finding, the proposed incidental take must not prevent a depleted population from increasing toward its OSP.” ... “If a particular stock were known to be within its OSP range, then the Service believes a finding of negligible impact can only be made if the permitted activities are not likely to reduce that stock below its OSP. However, not all takings that do not reduce the population below its OSP would be considered negligible.”).

In 1999, NMFS itself developed criteria for comparing incidental mortality levels to PBR lev