Full opinion text
ORDER LAWRENCE K. KARLTON, Senior District Judge. The remaining claims in this suit concern two dams and related water diversions on the Yuba River. The dams are operated by the Army Corps of Engineers (“Corps”). The river is home to populations of Chinook salmon, steelhead, and green sturgeon listed as threatened under the Endangered Species Act (“ESA”), 16 U.S.C. § 1531 et seq. In 2007, the National Marine Fisheries Service (“NMFS”) issued a Biological Opinion (“BiOp”) concluding that the Corps’ future operations would not violate the ESA. Plaintiffs, two environmental groups, claim that NMFS’s BiOp is arbitrary and capricious and that the Corps’ operations are causing take of protected salmon and steelhead. Remaining defendants in this case are NMFS, the Corps, and various federal officials, collectively the “Federal Defendants.” Pending before the court are four motions. In one, plaintiffs seek summary judgment solely on the issue of plaintiffs’ standing to bring their claims. Separately, plaintiffs and Federal Defendants have filed cross motions for summary judgment as to liability. Finally, plaintiffs seek a preliminary injunction pending final resolution of this suit. For the reasons stated below, the court concludes that plaintiffs have standing and that the BiOp is arbitrary and capricious. Plaintiffs’ claim regarding take raises two theories of liability. The court grants summary judgment to defendants as to the first and requests supplemental briefing as to the second. The court further requests supplemental briefing as to plaintiffs’ motion for a preliminary injunction, regarding mootness and the effect of the Supreme Court’s intervening decision in Monsanto Co. v. Geertson Seed Farms, — U.S. -, 130 S.Ct. 2743, 177 L.Ed.2d 461 (2010). I. Background A. The Endangered Species Act As recently reiterated by the Ninth Circuit, the ESA may be “ ‘the most comprehensive legislation for the preservation of endangered species ever enacted by any nation’ ” and “reflects ‘a conscious decision by Congress to give endangered species priority over the ‘primary missions’ of federal agencies.’ ” Cal. ex rel. Lockyer v. United States Dep’t of Agric., 575 F.3d 999, 1018 (9th Cir.2009) (quoting Tenn. Valley Auth. v. Hill, 437 U.S. 153, 180, 185, 98 S.Ct. 2279, 57 L.Ed.2d 117 (1978)). The ESA’s protection is triggered when species are “listed” as “threatened” or “endangered” by the applicable federal agency — in this suit, NMFS. ESA § 4(c); 16 U.S.C. § 1533(c); 50 C.F.R. § 402.01. “Species,” for purposes of the ESA, means not only taxonomic species, but also “any subspecies ... or distinct population segment of any species ... which interbreeds when mature.” ESA § 3(16); 16 U.S.C. § 1532(16). In the particular context of salmon, NMFS treats a population as a “species” if it is an “evolutionar[il]y significant unit,” (“ESU”) which is a population that is “substantially reproductively isolated from other conspecific population units; and [that] ... represents] an important component in the evolutionary legacy of the species.” Trout Unlimited v. Lohn, 559 F.3d 946, 950 (9th Cir.2009) (quoting Policy on Applying the Definition of Species, 56 Fed. Reg. 58,612, 58,618 (Nov. 20, 1991)). Three threatened species are at issue in this suit; the ESU of Central Valley spring run Chinook salmon (“spring run Chinook”), the distinct population segment of Central Valley steelhead (“steelhead”), and the southern distinct population segment of North American green sturgeon (“green sturgeon”). 50 C.F.R. §§ 223.102(c)(1), (c)(4), (c)(17). Plaintiffs invoke two of the ESA’s mechanisms for protecting listed species, sections 7(a)(2) and 9. Section 7(a)(2) provides that Each Federal agency shall, in consultation with and with the assistance of the Secretary [of Commerce or the Interi- or], 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 which is determined by the Secretary ... to be critical ESA § 7(a)(2); 16 U.S.C. § 1536(a)(2). In this suit, the Corps determined that the project was likely to affect the three listed species. Section 7 therefore obliged the Corps to seek a BiOp from NMFS regarding whether these effects exceed the limits set by section 7(a)(2). ESA § 7(b)(3); 16 U.S.C. § 1536(b)(3); 50 C.F.R. § 402.12(a), (k). That BiOp is the subject of plaintiffs’ third claim. The ESA also generally prohibits “take” of endangered species. ESA § 9(a); 16 U.S.C. § 1538(a). Roughly stated, whereas section 7 looks to populations, section 9 looks to individual organisms. ESA § 3(19); 16 U.S.C. § 1532(19). When a species is listed as threatened, rather than endangered, the Service must determine whether to apply section 9’s protections to the species. Id., see also ESA § 4(d); 16 U.S.C. § 1533(d). When this suit was filed, take of steelhead and spring run Chinook was largely prohibited, but take of green sturgeon was not. See 50 C.F.R. §§ 223.101, 223.203. ■ NMFS may relax the prohibition on take when take is incidental to activity for which NMFS has issued a “no jeopardy” BiOp. This relaxation takes the form of an “Incidental Take Statement,” which is a written statement that— (i) specifies the impact of such incidental taking on the species, (ii) specifies those reasonable and prudent measures that the Secretary considers necessary or appropriate to minimize such impact, (iii) ..., and (iv)sets forth the terms and conditions (including, but not limited to, reporting requirements) that must be complied with by the Federal agency or applicant (if any), or both, to implement the measures specified under clauses (ii) and (iii). ESA § 7(b)(4); 16 U.S.C. § 1536(b)(4). “[A]ny taking that is in compliance with the terms and conditions specified in a written [incidental take statement] ... shall not be considered to be a prohibited taking of the species concerned.” ESA § 7(o )(2); 16 U.S.C. § 1536(o )(2). B. Biology of The Three Species In reviewing the biology of the three species, the court relies on the November 2007 BiOp at issue in this suit (hereinafter “BiOp”), supplemented by the administrative record. 1. Spring Run Chinook Salmon Salmon are anadromous fish, meaning they hatch in freshwater streams, migrate to the ocean to mature, then return to freshwater to spawn. Spring run Chinook salmon generally begin their freshwater migration in January, reach their natal streams from March to July, hold in the river over summer, and spawn from August to October. BiOp at 6-7. This timing historically allowed spring run Chinook to spawn farther upstream than the more plentiful fall run, reproductively isolating the two populations. Id. at 25. Juvenile spring run Chinook typically spend a year or more in freshwater habitats before migrating downstream to the ocean. Id. at 6-7. For spawning, salmon require clean, loose gravel in swift, relatively shallow riffles (patches of stream with rough water), suitable depths and velocities for construction of redds (the gravel “nests” in which eggs are deposited), and adequate oxygenation for incubating eggs. Id. at 7. Juveniles need bank cover such as overhanging and submerged vegetation, root wads, and fallen woody debris. Id. at 7. Salmon are sensitive to water temperature throughout their life cycle. Id. at 6. According to documents included in the NMFS administrative record, “more than 20 ‘historically large populations’ of spring run chinook have been extirpated or reduced nearly to zero since 1940.” Admin. Record (“AR”) 11334-35 (Cal. Dept. of Fish and Game, “Fish Species of Special Concern in California,” at 39-40 (June 1995)) (hereinafter “Species of Special Concern”). The average abundance for the entire ESU was 12,590 for the period of 1969 to 1979, 13,334 for the period of 1980 to 1990, 6,554 from 1991 to 2001, and 16,349 since 2002. BiOp at 10. However, there is very little information regarding abundance within the lower Yuba River. Id. at 18-19. 2. Steelhead The BiOp explains that steelhead have life histories and habitat requirements that are similar to salmon, except that steel-head may spawn in multiple years. The BiOp discusses the needs of steelhead and spring run salmon together, referring to the species collectively as salmonids. Steelhead are also in similar decline. Historic populations were 1 to 2 million adults, reduced to about 40,000 in the early 1960s, to a spawning population of only about 3,600 female steelhead in 2005. BiOp at 11-12. 3. Green Sturgeon Like salmon and steelhead, green sturgeon migrate between the ocean and freshwater. BiOp at 9. Adults generally migrate upstream beginning in February and spawn between March and July. Id. Spawning requires deep, turbulent, cold-water pools with large cobble substrate. Id. Juveniles spend from one to four years in fresh and estuarine waters before dispersing to marine waters. Id. at 10. The mainstem Sacramento River population is the only remaining spawning population for the southern distinct population segment of the green sturgeon (the “species” at issue here). Id. at 9. The best available evidence indicates that range-wide green sturgeon abundance is currently declining, mainly due to loss of historic habitat caused by impassable dams. BiOp at 12; see also Proposed Threatened Status for Southern Distinct Population Segment of North American Green Sturgeon, 70 Fed. Reg. 17,386,17,391 (Apr. 6, 2005). C. The Challenged Project The project at issue here is the Corps’ “operations associated with Englebright and Daguerre Point Dams on the Yuba River in Yuba and Nevada Counties, CA.” BiOp at 2. This includes operation of the dams themselves, including the fish ladders at Daguerre Point Dam (“Daguerre”), together with the Corps’ “issuance of permits, licences and easements to non-Federal entities for their operations of water diversions and hydroelectric facilities at or near the dams.” Id. Non-federal actions permitted or licensed by the Corps include operation of two hydroelectric generation facilities at Englebright and three diversions in the vicinity of Daguerre — the Brown’s Valley, South-Yuba-Brophy, and Hallwood-Cordua diversions. Pursuant to a request by the Corps, NMFS issued the long-term biological opinion for this project on November 21, 2007. BiOp at 1. D. Procedural History Plaintiffs, the South Yuba River Citizens League and the Friends of the River, filed suit in December 2006, challenging a 2002 BiOp and bringing various other claims. After a protracted series of amendments and litigation of these other claims, the plaintiffs filed the operative Sixth Amended Complaint, which challenges the November 2007 BiOp described above. This complaint alleges four claims pertinent to the present motions. First, plaintiffs claim that NMFS acted arbitrarily and capriciously by adopting the BiOp in violation of section 7 of the ESA (plaintiffs’ third claim). Second, plaintiffs claim that the Corps violated section 9 of the ESA by operating the dams in a way that causes take, notwithstanding the fact that the BiOp includes an incidental take statement (plaintiffs’ fourth claim). This claim includes two theories of liability, which the Federal Defendants helpfully label as claims 4A and 4B. Claim 4A alleges that the incidental take statement was invalid ab initio, such that it could never shield the Corps from liability for take. Claim 4B alleges that the Corps has violated the terms and conditions imposed by the incidental take statement, thereby exceeding the scope of its protection. Third, plaintiffs argued that the Yuba County Water Agency (“YCWA”) violated section 9 for largely the same reasons — invalidity of the incidental take statement and the Corps’ failure to comply with the terms and conditions (plaintiffs’ sixth claim). Plaintiffs settled this claim concurrently with the filing of the motion for summary judgment on liability. Pursuant to this court-approved settlement, YCWA remains party to the case as an intervenor, and YCWA has filed briefs opposing plaintiffs’ motions. Various other non-federal entities have also intervened in this suit as defendants but largely have not filed briefing on the instant motions. Fourth and finally, plaintiffs claimed that NMFS had unreasonably delayed publication of rules protecting the green sturgeon under section 4(d) of the ESA. As noted above, the parties properly agree that this claim has been rendered moot by subsequent publication of such a 4(d) rule. Accordingly, the claims at issue are plaintiffs’ claim that the BiOp was arbitrary and capricious and plaintiffs’ claim that the Corps is causing take prohibited by section 9. II. Standing Constitutional standing requires that the plaintiff allege an injury in fact that is fairly traceable to the complained of harm and that is likely to be redressable by the court. Friends of the Earth, Inc. v. Laidlaw Envtl. Servs. (TOC), Inc., 528 U.S. 167, 180-81, 120 S.Ct. 693, 145 L.Ed.2d 610 (2000). Plaintiffs argue that they have standing because the organizations’ members regularly use the affected area of the Yuba River “for recreational, educational, aesthetic and spiritual enjoyment,” including interest in the listed species. These assertions are supported by declarations from individual members of the plaintiff organizations. Plaintiffs allege that the operations harm fish, limiting plaintiffs’ ability to derive enjoyment therefrom, and that a court order remanding the BiOp and enjoining take will protect fish and remedy this injury. Plaintiffs filed a motion solely seeking a judicial determination of the above. YCWA opposed this motion prior to settling the claims against it. YCWA argued, in essence, that because plaintiffs’ claims would fail on the merits, plaintiffs had failed to show injury sufficient to grant standing. This argument misconstrues the standing inquiry, the purpose of which “is to ensure that the plaintiff has a concrete dispute with the defendant, not that the plaintiff will ultimately prevail against the defendant.” Hall v. Norton, 266 F.3d 969, 976-77 (9th Cir.2001). Federal Defendants explicitly state that they do not dispute plaintiffs’ standing. Indeed, Federal Defendants argue that standing was not in dispute, such that plaintiffs should not be entitled to fees in connection with the above motion. Aside from noting that this argument is in some tension with YCWA’s decision to argue that plaintiffs lack standing, the court does not resolve this question here. The present questions regarding liability are complicated enough that discussion of fees may be postponed to another day. Federal Defendants further argue that plaintiffs’ freestanding motion on standing is procedurally improper. The Ninth Circuit has not addressed whether Fed.R.Civ.P. 56 permits a motion seeking partial adjudication of issues other than liability. An apparent majority of courts outside the Ninth Circuit, including the Second, Third, and Seventh Circuits, have held that a motion for summary judgment must seek a judicial determination that at least fully resolves liability on a claim. Under that rule, a defendant may move for summary judgment solely on the ground that a plaintiff lacks standing, but a plaintiff may not bring a converse motion because granting the latter would not determine liability on the claim. Most district courts within the Ninth Circuit, however, have held that Rule 56 permits motions of the latter type. In the context of the pending cross-motions on liability, the court may plainly determine standing; indeed, the court has an independent obligation to do so. Accordingly, the procedural argument raised by the Federal Defendants is only relevant to plaintiffs’ potential fee recovery. Again, the court postpones this issue until another day. III. Liability Plaintiffs’ third claim argues that NMFS’s BiOp is arbitrary and capricious in its no-jeopardy conclusion, in its critical habitat designation, and in the attached incidental take statement. The court agrees with these ultimate conclusions, although the court rejects some of plaintiffs’ underlying arguments. Plaintiffs’ fourth claim argues that the Corps has caused take. The court rejects the legal theory underlying claim 4A, that the incidental take statement was void ab initio. As to claim 4B, it appears that factual questions remain, but that this claim has been rendered moot. A. Standards of Review Plaintiffs’ various arguments regarding the sufficiency of the BiOp challenge final agency actions subject to “arbitrary and capricious” review under the Administrative Procedure Act. 5 U.S.C. § 706(2)(A); Bennett v. Spear, 520 U.S. 154, 178, 117 S.Ct. 1154, 137 L.Ed.2d 281 (1997). Under such review, the court does not employ the usual summary judgment standard for determining whether a genuine issue of material fact exists. Conservation Cong. v. United States Forest Serv., 555 F.Supp.2d 1093, 1100 (E.D.Cal.2008). This is because the court is not generally called upon to resolve facts in reviewing agency action. Occidental Eng’g Co. v. INS, 753 F.2d 766, 769-70 (9th Cir.1985). Instead, the court’s function 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. The APA authorizes the court to set aside agency action that is “arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with the law.” 5 U.S.C. § 706(2)(A); Nw. Envt’l Def. Ctr. v. Bonneville Power Admin., 477 F.3d 668, 682 (9th Cir.2007). An agency decision is arbitrary and capricious where the agency “relied on factors Congress did not intend it to consider, entirely failed to consider an important aspect of the problem, or offered an explanation 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.” Lands Council v. McNair, 537 F.3d 981, 987 (9th Cir.2008) (en banc) (quotations omitted). The agency “must articulate a rational connection between the facts found and the conclusions reached.” Earth Island Inst. v. United States Forest Serv., 442 F.3d 1147, 1157 (9th Cir.2006) (citing Midwater Trawlers Co-op v. Dep’t of Commerce, 282 F.3d 710, 716 (9th Cir.2002)). This relatively deferential standard is especially appropriate when reviewing factual determinations that implicate an agency’s scientific expertise. Ariz. Cattle Growers’ Ass’n v. United States Fish & Wildlife, BLM, 273 F.3d 1229, 1236 (9th Cir.2001). Even for scientific questions, however, a court must intervene when the agency’s determination is counter to the evidence or otherwise unsupported. See, e.g., Sierra Club v. United States EPA, 346 F.3d 955, 962 (9th Cir.2003), amended by 352 F.3d -1187 (9th Cir.2003) (rejecting agency’s factual conclusion about cause of air quality exceedance). Plaintiffs’ fourth claim, which alleges that the Corps has caused take, is not wholly subject to arbitrary and capricious review, as explained by the court’s Order filed December 23, 2008 (Dkt. No. 184). In that order, the court explained that plaintiffs’ claim that the incidental take statement was invalid (claim 4A) would be subject to arbitrary and capricious review no matter how that argument was packaged. Order at 19-20. The allegations that the defendants had violated the terms and conditions of the incidental take statement and actually caused take (claim 4B), however, require the court to look beyond the administrative record. Id. at 21. The latter allegations therefore implicate the ordinary summary judgment standard under Fed.R.Civ.P. 56. Because the court’s analysis of this claim requires only fleeting discussion of this standard, the court does not repeat it here. B. Jeopardy Analysis The BiOp concludes that the project will not “jeopardize the continued existence of’ listed species. See ESA § 7(a)(2); 16 U.S.C. § 1536(a)(2). In part, plaintiffs challenge the sufficiency of NMFS’s analysis, alleging that NMFS failed to consider aspects of the problem or to explain the basis for its conclusions. See Sixth Amended Complaint ¶¶ 101, 104-09. Beyond these “show your work” arguments, plaintiffs argue that the evidence compelled a jeopardy conclusion. See id. ¶¶ 102-03. Upon careful review, the record demonstrates that NMFS has not supported its position, but not that a jeopardy conclusion was inescapable. The applicable regulations define “jeopardize the continued existence of’ to mean “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; see also Nat’l Wildlife Fed’n v. NMFS, 524 F.3d 917, 933 (9th Cir.2008) (survival and recovery are distinct). The BiOp provides “genetic and life-history diversity” as a fourth criteria, and the court defers to NMFS’s interpretation of its own regulation here. BiOp at 32. Coeur Alaska, Inc. v. Se. Alaska Conservation Council, — U.S. -, - 129 S.Ct. 2458, 2468, 174 L.Ed.2d 193 (2009) (citing Auer v. Robbins, 519 U.S. 452, 461, 117 S.Ct. 905, 137 L.Ed.2d 79 (1997)). Federal Defendants correctly note that both “jeopardize” and “reduce” are verbs. “Agency action can only ‘jeopardize’ a species’ existence if that agency action causes some deterioration in the species’ pre-action condition.” Nat’l Wildlife Fed’n, 524 F.3d at 930 (emphasis added). Although the focus of the jeopardy inquiry is on the effects of agency action, these effects can only be understood in context. This context includes “the current status of the listed species,” the “environmental baseline,” and future “cumulative effects.” 50 C.F.R. §§ 402.02, 402.14(g)(2)-(3). The regulations define the environmental baseline to include “the past and present impacts of all Federal, State or private actions and other human activities in the action area” and “the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultation.” 50 C.F.R. § 402.02. Cumulative effects are “those effects of future State or private activities, not involving Federal activities, that are reasonably certain to occur within the action area of the Federal action subject to consultation.” Id. In light of the complexity of this case, the court summarizes its analysis of the no-jeopardy conclusion before discussing the issues in detail. Plaintiffs argue that numerous effects of the project, the environmental baseline, and future non-federal projects are harmful to listed species. Some, but not all, of these effects are recognized by the BiOp. As Federal Defendants now characterize it, the BiOp concludes that these recognized effects would not jeopardize the species because (1) the local populations of the three listed species are “stable” notwithstanding these ongoing harmful effects, (2) to the extent that the project changes local conditions, these changes will be favorable to local populations of listed fish, and (3) various future projects will further benefit the three species. Fed. Defs.’ Summ. J. Mem. at 10,14. In other words, if the status quo is acceptable and the project will improve conditions, the project will not jeopardize the species. The court cannot accept this argument because, contrary to Federal Defendants’ arguments in this litigation, the BiOp does not conclude that local populations are stable. Without this predicate, the BiOp offers no basis for concluding that the project’s unmitigated effects would not jeopardize the species. The BiOp therefore fails to provide a “rational connection” between the facts found and the no-jeopardy conclusion. Earth Island Inst., 442 F.3d at 1157. Separate from this argument, plaintiffs argue that the BiOp failed to discuss various other effects caused by the project or constituting part of the environmental background, thereby failing to consider important aspects of the problem. McNair, 537 F.3d at 987. If the species were found to be stable, a top-down analysis predicated on stability might have rendered discussion of these omitted impacts unnecessary. Absent such a finding, many of these effects were sufficiently “important” to require discussion. 1. Effects Recognized by the BiOp The court begins with the BiOp’s discussion of effects of the project and the environmental baseline harmful to listed fish. Federal Defendants refer to these effects as “stressors.” The stressors recognized by the BiOp include impairments to migration, effects on flow regimes, effects on spawning habitat, and entrainment and impingement at diversions. Although these categories are not wholly distinct, they provide structure to the analysis. With the apparent exception of effects on regulated flow regimes, the BiOp attributes all of the following stressors to the project rather than the baseline. a. Migration Barriers The primary effects on migration stem from Daguerre Point Dam and Englebright Dam. i. Daguerre Point Dam’s Effect on Migration Daguerre, the smaller and farther downstream of the two dams within the project area, detrimentally affects both upstream and downstream migration. Beginning with upstream migration, although the dam itself blocks upstream fish passage, salmonids (but not sturgeon) may circumvent this barrier through two fish ladders. These ladders were most recently “reconstructed” in 1964. Fed. Defs.’ Statement of Undisputed Facts # 23. The BiOp acknowledges four problems with these ladders, three of which the project attempts to mitigate. BiOp at 26. First, the ladders must be closed entirely at high flows. IcL; see also AR 12793 (U.S. Army Corps of Engineers, Sacramento District, “Daguerre Point Dam, Yuba River, California, Preliminary Fish Passage Improvement Study,” at 12 (August 2001)) (hereinafter “Preliminary Passage Study”) (explaining that ladders must be closed at flows over 15,000 cubic feet per second). The BiOp does not describe the duration of these closures, but evidence in the record indicates that the duration can exceed a month. AR 4614 (Cal. Dept. Fish and Game, “A Status Review of the Spring Run Chinook Salmon (Oncorhyncus Tshawytscha) in The Sacramento River Drainage,” at § VII p. 49 (June 1998)) (hereinafter “Spring Run Chinook Status”). High flows coincide with the conditions under which spring run Chinook and steelhead migrate upstream. BiOp at 26. Second, when flows are high but not so high as to require closure of the ladders, fish have difficulty finding the ladders. Id. Fish find the ladders because of the water flowing down them, which forms an “attraction flow.” During high flows, “a very small percentage of attraction flows eom[es] out of the ladders compared to the massive sheet flow coming over the dam. The angle of the orifices and proximity to the plunge pool also increases the difficulty for fish to find the entrances to the ladders.” Id., see also id. at 22 (“Daguerre Point Dam includes suboptimal ladder design and sheet flow across the dam spillway that may obscure attraction to the ladder entrances, particularly during high flow periods”), AR 12793 (Preliminary Passage Study at 12). Since 2001, the Corps has attempted to mitigate this problem by installing seasonal flash boards that direct additional flows toward the ladders. BiOp at 22. The BiOp asserts that monitoring data since 2006 indicates that this has “resulted in an immediate and dramatic increase in the passage of salmon up the ladders.” Id. Upstream migration is also hampered when woody debris collects in the ladders. Id. (debris “clog[s]” the ladders). The Corps has installed a log boom to keep debris out of the northern ladder (where the problem is more severe), and the Corps and/or the California Department of Fish and Game (“DFG”) ordinarily inspects both ladders weekly in order to clear out debris. Id. at 22, 32-33. The fourth barrier to upstream migration at Daguerre is the formation of a gravel and sediment bar immediately upstream from the fish ladders. BiOp at 22. Gravel buildup can itself block fish passage, as well as further reduce attraction flows on the ladders. Id. at 22. The Corps has implemented a plan to ensure that a 30 foot by 3 foot channel remains open to facilitate fish passage and avoid blocking attraction flows. Id. Although the Corps has attempted to ameliorate the above four impediments to upstream migration, the BiOp does not take a clear position on the efficacy of these efforts. The BiOp states that “[u]p-stream passage conditions at Daguerre Point Dam are .,. considered inadequate for Chinook salmon and steelhead throughout much of the year” and that “[u]p-stream passage at Daguerre Point Dam is often problematic for migrating salmonids due to inadequacies of the fish ladders.” Id. at 26, 31. These statements use the present tense, and occur in the BiOp’s discussion of the effects of the action. Thus, the BiOp indicates that the recent efforts have not totally cured these inadequacies and problems. The BiOp notes that even when salmonids successfully navigate the fish ladders, the ladders’ inadequacies often delay migration, which depletes salmonids’ energy stores, makes fish susceptible to predation, decreases egg viability, and changes the spatial distribution of spawners. Id. at 27, 31. Daguerre also interferes with downstream migration. Id. at 27. “The large pool at the base of the dam creates an area of unnatural advantage for predatory fish ... where juvenile salmonids can be disoriented or injured as they plunge over the face of the dam into the turbulent waters at the base.” Id. The BiOp does not describe any actions taken to mitigate this effect. ii. Englebright Dam’s Effect on Migration The farther upstream of the two dams in the project is Englebright Dam. The BiOp states that “[t]he greatest impact to listed salmonids associated with the Corps’ operations on the Yuba River” is the absolute barrier to migration posed by Englebright dam. BiOp at 31. Englebright contains no fish ladders. Id. at 2, 25. This prevents access to otherwise suitable habitat for salmonids. “[T]he majority of historical spawning and holding habitat for spring-run Chinook salmon and steelhead occurred above Englebright Dam.” Id. at 25. Blocking access to this habitat not only decreases the total amount of available habitat, it also increases the spatial overlap between spring run and fall run Chinook, allowing the species to interbreed and thereby decreasing the species’ genetic diversity. Id. at 25. Later-spawning fall run Chinook can also physically disrupt spring run eggs by digging spawning redds in locations where spring run eggs are incubating. Id. Another dimension of this impact is that by concentrating populations, Englebright increases the populations’ susceptibility to a catastrophic event such as a chemical spill or massive flood. Id. The BiOp discusses no efforts to mitigate these impacts. The parties dispute whether, for purposes of the jeopardy analysis, Englebright’s prevention of migration is an effect of the project or instead part of the baseline. As noted above, section 7 prohibits federal agency action that would “jeopardize” species. The section 7 analysis therefore looks to effects on species caused by agency action. Nat’l Wildlife Fed’n, 524 F.3d at 930. Effects not attributable to agency action, whether directly or indirectly, cannot themselves demonstrate a violation of section 7. In another case concerning ongoing dam operation, the Ninth Circuit explained that “existence of the dams must be included in the environmental baseline” of effects that are not “caused” by the project under consideration. Id. at 931. Where the federal agency retains discretion regarding a dam’s operation, however, section 7 requires consideration of whether effects attributable to this operation jeopardize the species. Id. This distinction is easy to state but hard to apply. In this case, the Federal Defendants argue that Englebright Dam’s effect as a migration barrier results from the existence of the dam. Plaintiffs contend that this effect is attributable to the Corps’ ongoing operation of the dam, which plaintiffs contend should include provision of a fish ladder to enable upstream migration, a service to involuntarily transport juveniles to enable downstream migration, and various other efforts included in the operation of some analogous dams. Regardless of the Federal Defendants’ litigation position, the BiOp itself discussed Englebright’s prevention of future migration as part of the analysis of the “effects of the action,” rather than as part of the baseline, distinguishing these future effects from past effects on migration. BiOp at 18, 25. Even if the BiOp could have used a different assumption, that possibility does not provide a basis for upholding the decision the agency actually made. Motor Vehicle Mfrs. Ass’n v. State Farm Mut. Auto. Ins. Co., 463 U.S. 29, 50, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983) (“an agency’s action must be upheld, if at all, on the basis articulated by the agency itself.”). Alternatively, even if the court were to conclude that the BiOp treated these future effects as part of the baseline and that this treatment was permissible under the ESA, the BiOp’s jeopardy analysis would still be deficient. Assuming that there was some method by which the court could ‘subtract out’ Englebright’s impacts on migration and attribute these to the baseline, the BiOp would still fail to adequately discuss the other unmitigated stressors. b. Flow Regimes and Temperature “Low Summer flows (both natural and controlled)” in the project area “can cause elevated water temperatures in spring-run holding and spawning habitat, resulting in pre-spawning mortality and reduced reproductive success.” BiOp at 17. Salmon and steelhead at all life stages are harmed by these increased temperatures. Id. at 6. Englebright formerly contributed to this problem in two ways, although the BiOp concludes that the first has been ameliorated. This first effect was through irregularity, as Englebright would periodically (and unexpectedly) halt flows. Id. at 22. Englebright releases water almost exclusively through two hydroelectric facilities. Id. at 2. Historically, when these facilities unexpectedly shut down — whether accidentally or because of an emergency— downstream flows were immediately and drastically curtailed, with harsh effects on downstream salmonids. Id. at 22. In 2006, a flow bypass system was installed in the larger of the two powerhouses, which allows 88% of that facility’s flow to be released in event of a shutdown. Id. The BiOp concludes that this eliminated the problem of unexpected flow disruption. Id. at 23. Separate from the problem of unexpected flow interruption, the scheduled releases from Englebright and Daguerre can be “insufficient” for listed species. Id. at 17. This problem results from diversion of water to other users. Id. at 23. Plaintiffs have not argued that the Corps has authority over these flow regimes, and thus the court accepts the BiOp’s attribution of 26 this effect to the environmental baseline. Id. at 17. The BiOp indicates that this stressor has been partially ameliorated. A decision of the California State Water Resources Control Board in 2003 imposed “new minimum flow requirements and flow fluctuation criteria on the lower Yuba River.” Id. These flows “did not provide the level of flow protection recommended by DFG or NMFS,” although they constituted an improvement over prior practice. Id. at 23-24. More recently, the Yuba Accord Fisheries Agreement (“Yuba Accord”) proposes to further “manag[e] flows from ... Englebright Lake to further enhance critical habitat and water temperature in the Yuba River.” Id. at 4-5, 24. The benefits of this management extend to the “lower Yuba River,” and thus appear to encompass areas below Daguerre as well as areas immediately below Englebright. Id. at 24. The Yuba Accord’s flow schedules were adopted on an interim basis in 2005. Id. In 2007, when the BiOp was adopted, the agreement was “expected to be finalized and implemented in early 2008.” Id. The new management “improve[s] flow schedules” for fish, providing benefits “that are at least equal to but often greater than” those provided by 2003 schedules. Id. at 24. As with other mitigation efforts, however, the BiOp does not quantify this improvement. In particular, the BiOp’s statements comparing the Yuba Accord flows and the 2003 flows suggest that the neither regime meets the recommendations of NMFS or DFG. Insofar as these flow regimes fall short of those recommended by NMFS, they apparently constitute a continuing stressor. c. Gravel and Spawning Habitat Englebright limits recruitment of gravel and large woody material. As noted above, salmonids require clean gravel beds in which to spawn. Woody material is also necessary for the protection of salmonids as it provides a cover from predators and a velocity refuge. BiOp at 7-8. Historically, the river would carry these materials downstream past the dam site, but these materials are now trapped behind the dam. Id. at 26. Englebright’s elimination of this effect “has practically eliminated viable spawning habitat in the area immediately below the dam [and] down through the Narrows Canyon,” and this effect is felt to a lesser degree throughout the river below the dam. Id. at 29. In response to Englebright’s interference with gravel recruitment, the Corps planned to adopt a gravel augmentation program, which injects additional gravel into the river. Id. at 5. At the time the BiOp was prepared, this program had not yet begun. Id. The BiOp does not indicate that Daguerre separately interferes with gravel, and plaintiffs do not contend that this is the case. The incidental take statement requires a similar program for injecting woody material below Englebright. Id. at 40. This program has not yet begun, and neither party discusses its potential effectiveness. See, e.g., Fed. Defs.’ Statement of Undisputed Facts # 64. d. Entrainment and Impingement Where water is diverted, a screen is used to keep fish from being “entrained,” i.e., diverted from the river to the diversion channel. Although these screens are necessary to protect fish, they also present a risk to fish, as fish can be “impinged,” i.e., trapped against the screen by the force of water. The BiOp criticizes the screen at the South-Yuba/Brophy diversion above Daguerre as presenting both risks. This screen “fails to meet many of the criteria developed by NMFS and DFG for adequate fish screen operation and fish safety.” BiOp at 28. Specifically, the interstitial spaces between rocks making up the weir are large enough to let fish through, there is no adequate “sweeping flow” which can prevent impingement, and juvenile salmonids become “entrained behind the barrier either by passing through the weir or being washed over the top during high flows.” Id. The BiOp noted that the Corps was working to remedy these problems, but that “there [were] no guarantees that a new screen [would] be constructed.” Id. Two other diversions have superior screens. The Brown’s Valley Diversion, built in 1999, is “state of the art[,] ... meets all current NMFS and DFG screening criteria[,] and is no longer considered to pose a threat to entrainment of juvenile salmonids.” Id. at 28. The Hallwood-Cordua diversion was rebuilt in 2000. Id. at 28. The screen still “does not fully meet all DFG and NMFS criteria,” but the rebuilding “greatly improved the effectiveness of the screen.” Id. 2. Whether The Recognized Stressors Jeopardize the Species’ Likelihood of Survival As the above shows, the BiOp recognizes that numerous mechanisms stress listed fish. In this litigation, Federal Defendants argue that the BiOp identified measures that would “greatly decrease[ ],” “significantly ameliorate! ],” and “substantially mitigate” the effects of some stressors. These efforts target only a narrow subset of the stressors affecting listed species. See Fed. Defs.’ Summ. J. Mem. at 15 (conceding this point). Even for the ameliorated stressors, the BiOp suggests that amelioration is wholly successful for only two, the fish screen at the Brown’s Valley diversion and the flow bypass mechanism at the Narrows II powerhouse. Thus, of the effects the BiOp attributes to the proposed action, Englebright’s prevention of migration, Daguerre’s interference with downstream salmonid migration, and Daguerre’s prevention of sturgeon migration are wholly unmitigated. Mitigation is only partial with regard to Daguerre’s impacts on upstream salmonid migration and fish screening at the Hailwood Cordura diversion. Brophy’s problems with entrainment and impingement and the dams’ effects on deposition of gravel and wooden material have not yet been mitigated. The BiOp also indicates that problems with flow regimes have not been fully eliminated, such that flows continue to stress fish, but the BiOp apparently treats this stressor as part of the baseline. Imposition of a stressor on a species does not necessarily decrease the reproduction, numbers, distribution or diversity of the local population. In principle, for example, any stretch of stream has a finite carrying capacity for juvenile salmonids. If, notwithstanding a migration barrier, the number of adults reaching the spawning ground each year is sufficient to produce juveniles in excess of this capacity, then the migration barrier may not reduce the local population. See, e.g., U.S. Fish & Wildlife Serv. & Nat’l Marine Fisheries Serv., Endangered Species Consultation Handbook: Procedures for Conducting Consultation and Conference Activities Under Section 7 of the Endangered Species Act 4-24 to 4-25, 4-30 to 4-31 (1998) (hereinafter “Section 7 Handbook”) (describing populations’ abilities to absorb some impacts). NMFS’s handbook contemplates a method of analysis wherein NMFS will calculate the magnitude of the stressor and then determine whether the local population can absorb this impact without a long-term decline. Id. This inquiry is obviously context sensitive, as exposure to one stressor limits a population’s ability to tolerate others. Even where stressors will cause a decline in one or more of the four viability factors identified by the BiOp, the magnitude of this decline may be low enough that the decline does not jeopardize the species as a whole. See, e.g., Selkirk Conservation Alliance v. Forsgren, 336 F.3d 944, 957 (9th Cir.2003) (upholding BiOp’s conclusion that although project’s impacts were incompletely mitigated, they were mitigated enough so as to avoid jeopardizing the species at issue); see also Butte Envtl. Council v. United States Army Corps of Eng’rs, 607 F.3d 570, 580-81 (9th Cir.2010) (reaching a similar conclusion for critical habitat analysis). The court therefore turns to the BiOp’s analysis of whether the stressors imposed by the proposed project would jeopardize the species’ survival. The court quotes this analysis at length: Lack of access to diverse habitats upstream of the dams reduces all four viability factors (abundance, productivity, spatial structure and genetic diversity) for these species. Juvenile losses from diversions, predation, and low-quality rearing habitat affect abundance and productivity of the populations. Reductions in spawning gravels affect productivity and spatial structure of the species, and the forced overlap of spawning habitat between spring-run and fall-run Chinook salmon affects the genetic diversity of the threatened spring-run Chinook salmon. It is likely that the facilities and operational procedures used in the past, if left uncorrected, would cause continued declines in population viability of these species and in the conservation value of critical habitat. However, there have been several recent changes to the facilities and operational procedures related to the Corp’s Yuba River operations which are expected to improve conditions for Yuba River fisheries. And recent salmonid monitoring data, while insufficient to allow detection of definite trends, do not suggest any significant, ongoing decline of salmonid populations or habitat variables in the lower Yuba River. In considering the current baseline conditions, future cumulative effects, and the above listed recent actions taken to improve conditions on the lower Yuba River, NMFS has determined that the level of effects caused by Corps operations will be unlikely to cause a reduction in the population numbers, reproductive success or the distribution of listed fish in the Yuba River to the point of appreciably reducing these populations’ likelihood of survival into the future. BiOp, 32-33. In the omitted passage of this analysis, the BiOp summarizes six “recent actions” referred to in the second and third paragraphs quoted above: improvements to the Browns Valley and Cordura Hailwood diversions, use of flash boards at Daguerre, debris cleaning at the Daguerre ladders, channel cleaning upstream of Daguerre, and use of a flow bypass system at the larger powerhouse below Englebright. As noted above, these six changes do not fully ehminate the project’s impacts. Plaintiffs argue that without discussing the magnitude of the unmitigated stressors’ impact, the BiOp cannot support the conclusion that these impacts will not jeopardize the species. Federal Defendants argue that although the BiOp did not discuss the impacts of the unmitigated stressors individually, the BiOp considered their net effect. It appears that NMFS may employ an analytic method that captures aggregate impact without discussing impacts individually. In Selkirk, plaintiffs claimed that the BiOp failed to discuss future private forestry projects as part of the cumulative effects analysis. 336 F.3d at 964. Rather than discuss individual projects separately, the BiOp in Selkirk had analyzed an umbrella agreement governing these projects. The Ninth Circuit rejected plaintiffs’ claim, holding that the Fish and Wildlife Service did not need to “list, detail, and discuss” every individual project so long as it employed a device that accurately captured their cumulative effects, and that the umbrella agreement discussed in that case was such a device. Id. This caveat is crucial. A broad-level analysis is impermissible where it will mask individual effects rather than measure them. Pac. Coast Fed’n of Fishermen’s Ass’ns v. NMFS, 265 F.3d 1028, 1036-37 (9th Cir.2001) (analysis on a large spatial scale insufficient to support no-jeopardy opinion where scale would ignore “projects with a relatively small area of impact but that carried a high risk of degradation,” which might have significant aggregate impacts). The BiOp in this case does not explicitly adopt a net impacts analysis. At most, the discussion of population monitoring data in the analysis quoted above provides some implication of such an approach. In briefing the present motions, Federal Defendants argue that the BiOp determined “that populations on the Yuba are at least stable, and that the actions proposed as part of the project are likely to improve habitat quality.” Fed. Defs.’ Summ. J. Mem. at 14. If NMFS had concluded that populations were stable in recent history despite the persistence of stressors, this would provide some indication that the populations could withstand the stressors. Because the stressors discussed above will be no worse than those in recent history, it would follow that the project would not cause a decline. Contrary to defendants’ litigation position, however, the BiOp carefully avoids reaching the underlying conclusion of stability. The BiOp simply notes that the data do not allow for detection of “definite trends” and that the data “do not suggest any significant, ongoing decline of salmon-id populations or habitat variables.” BiOp at 32. The BiOp does not discuss population trends for green sturgeon at all. The statement that the data “do not suggest any significant, ongoing decline” does not mean that the data “suggest that populations are not in significant, ongoing decline” or “suggest that salmonid populations are stable.” No such affirmation of stability appears in the BiOp, nor have Federal Defendants cited such a statement in the administrative record. In sum, while the data “do not suggest” a decline, that is because they are so inconclusive that they “do not suggest” anything at all. Presumably in recognition of this problem, at oral argument Federal Defendants explicitly disclaimed any reliance on population trend data in the BiOp’s jeopardy analysis. Federal Defendants have not identified any other method of net effects analysis. The court further notes that the BiOp itself concludes that survival and recovery must be evaluated in light of four viability factors, but Federal Defendants’ “stability” argument appears to implicate only one of these factors, abundance. The available data appear to be limited to monitoring at the Daguerre fish ladders. Neither the BiOp nor Federal Defendants explain how such data measures productivity, spatial distribution or genetic diversity. BiOp at 32, see also Fed. Defs.’ Statement of Undisputed Facts # 36 (discussing monitoring data’s indications of abundance, but not other factors). Accordingly, the BiOp recognizes that past practices have caused a decline, recognizes that some of these practices (including numerous effects attributed to the action itself) are ongoing but have not been fully mitigated, and ultimately concludes that “the level of effects caused by Corps operations will be unlikely to cause a reduction in the population numbers, reproductive success or the distribution of listed fish in the Yuba River to the point of appreciably reducing these populations’ likelihood of survival into the future.” BiOp at 33. Without more, this does not provide a “rational connection between the facts found and the conclusions reached.” Earth Island Inst., 442 F.3d at 1157. In a case considering whether NMFS had properly concluded that its proposed “reasonable and prudent alternatives” (“RPA”s) would avoid jeopardy, the Ninth Circuit explained that mere recognition of RPA’s effects accompanied by a statement that these effects will not jeopardize a species is insufficient. Pac. Coast Fed’n of Fishermen’s Ass’ns v. United States Bureau of Reclamation, 426 F.3d 1082, 1092 (9th Cir.2005). In another case concerning dam operation, where the BiOp conceded that the project would cause “significant” impairments to habitat, the BiOp could not conclude that these impairments would not jeopardize survival or recovery without knowing “in-river survival levels necessary to support recovery” and “at what point survival and recovery will be placed at risk” by habitat degradation. Nat’l Wildlife Fed’n, 524 F.3d at 936; see also Bennett, 520 U.S. at 176, 117 S.Ct. 1154 (jeopardy analysis cannot be “on the basis of speculation or surmise.”). In order to determine that the stressors will not cause a decline in reproduction, population, distribution, or diversity, the BiOp must discuss (through some method) the magnitude of the stressors’ impact, the populations’ ability to tolerate this impact, and the reason why any decline will not reduce the overall likelihood of survival or recovery. A court “cannot simply take the agency’s word that the listed species will be protected under the planned operations: ‘If this were sufficient, the NMFS could simply assert that its decisions were protective and so withstand all scrutiny.’ ” Id. at 935 n. 16 (quoting Pacific Coast Fed’n, 426 F.3d at 1092). Accordingly, although the BiOp properly concludes that the project, as proposed in 2007, will partially reduce the impact of prior stressors, this is itself insufficient. Because the BiOp concludes that the project will continue to impose stressors on listed species without explaining why these stressors will not jeopardize the species, the BiOp’s no-jeopardy conclusion is arbitrary and capricious. 3. Cumulative Effects Discussed by the BiOp As noted above, the jeopardy analysis must include discussion of “cumulative effects,” i.e., “effects of future State or private activities, not involving Federal activities, that are reasonably certain to occur within the action area of the Federal action subject to consultation.” 50 C.F.R. § 402.02. Especially where, as here, the federal project imposes stressors on the listed species, the jeopardy analysis must consider both whether-the species is currently able to tolerate the stressor and whether the species will continue to be able to do so in light of future non-federal actions. Plaintiffs challenge the BiOp’s discussion of one source of cumulative effects, YCWA’s proposed Wheatland project. See BiOp at 29. At the time the BiOp was adopted, YCWA had proposed and received funding for this project, which would divert an additional 41,000 acre-feet of water annually through the Brophy diversion in order to supply various agricultural users. Id. Because the effects of the Wheatland project have not yet occurred, such effects could not be captured by the net effects analysis proffered by Federal Defendants in this litigation. The Wheatland project will alter flow regimes and will aggravate problems at the Brophy fish screen. Beginning with flow regimes, the BiOp predicts that the Wheatland project will increase flows between Daguerre and Englebright during the summer, as additional water is released from Englebright to supply the diversion. Id. at 30. These increased flows “in the primary spawning and rearing reaches” above Daguerre are expected to benefit salmonids. Id. The Wheatland project will also decrease summer flows below Daguerre. Although this decrease should only occur when flows exceed minimum flow requirements, this reduction is nonetheless expected to have an adverse impact. Id. The BiOp reasoned that as for salmon-ids, Wheatland’s adverse effects on flows below Daguerre would be offset by Wheat-land’s beneficial effects above. Id. The court disagrees with plaintiffs’ argument that this conclusion is unsupported by the record. The BiOp discusses the particular impacts above and below Daguerre before qualitatively comparing the two, and the court cannot determine that this conclusion was arbitrary or capricious. Left out of this discussion, however, are the green sturgeon, which are confined below Daguerre. Accordingly, the BiOp did not support its conclusion that the Corps’ operations, when considered in the context of the future Wheatland project, will not jeopardize the green sturgeon. Separate from the effects on flow regimes, the Wheatland project will aggravate the existing problem of entrainment at the Brophy diversion by increasing flows diverted there. The BiOp concludes that “the expected 40 percent increase in entrainment at the South Yuba-Brophy diversion is expected to cause a reduction in survival of juvenile steelhead and spring-run Chinook salmon in the Yuba River.” BiOp at 30 (emphasis added). The BiOp does not explain why the Corps’ activities, when combined with this increase in entrainment, will not jeopardize the listed salmonids. Id. at 33, 38 (asserting without further discussion that the combined effects will not appreciably reduce the species’ likelihood of survival or recovery). The BiOp does note that “[t]he Corps has been participating with the Brophy Irrigation District, NMFS, DFG, and the FWS to investigate, design, and implement an economical plan to replace the current rock weir screening device on the South Yuba-Brophy Diversion with a new positive barrier fish screen that will meet all current CDF and NMFS fish screen criteria for anadromous salmonids.” BiOp at 36. The BiOp explicitly recognized, however, that it was uncertain whether or when such a screen would be constructed. Id. at 28. The BiOp’s jeopardy analysis did not rely on completion of this screen, instead merely concluding that the proposed project would not interfere with such completion. Id. at 36. Although a term and condition of the incidental take statement was that “the Corps shall diligently pursue the ongoing effort to fully screen the South Yuba Brophy irrigation diversion to meet all DFG and NMFS screening criteria,” id. at 40, the BiOp does not guarantee or require that this screen be completed before the Wheatland project is implemented. Accordingly, the BiOp leaves open the possibility of a period of increased entrainment, and the BiOp does not analyze the effects of this period. This omission renders the BiOp arbitrary and capricious. Pac. Coast Fed’n of Fishermen’s Ass’ns, 426 F.3d at 1091 (failure to discuss effects that will occur prior to implementation of mitigation measures arbitrary and capricious). 4. Stressors Allegedly Not Discussed by The BiOp Separate from all the above, plaintiffs argue that the BiOp arbitrarily and capriciously failed to discuss hatcheries, the San Francisco Bay Delta, the species’ overall depressed conditions, global warming, and poaching. Plaintiffs contend that these omissions demonstrate that NMFS “failed to consider ... important aspect[s] of the problem,” McNair, 537 F.3d at 987, and that NMFS violated the ESA’s mandate to use the “best scientific and commercial data available.” ESA § 7(a)(2); 16 U.S.C. § 1536(a)(2). Plaintiffs rely on the “Lindley Study” in support of many of these arguments. This study, titled “Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin,” was published by the California Bay-Delta Authority Science Program and the John Muir Institute of the Environment in February of 2007. Lead author Steven T. Lindley, together with three more of the study’s twelve authors, are NMFS scientists. NMFS did not include this study in the administrative record. NMFS disputes whether the court may coijsider this study in a record review case and whether the study constitutes “best available science” that NMFS was obliged to consider. Because these questions are fact specific, the court addresses them in the context of specific omitted issues. The apparent threshold issue, to which the parties have paid little attention, is the determination of what constitutes an important aspect of the problem. Plainly, some issues are so obviously insignificant that NMFS’s silence thereon is not arbitrary and capricious. No reasonable layperson would expect that continental drift, changes in the stock market, or bad vibes from those in the area are significantly impacting fish on the Yuba River, and absent scientific evidence contradicting this lay expectation, NMFS need not explain why these issues are irrelevant. It appears just as plain, however, that important issues are not only those actually imposing significant effects on the species. NMFS must sometimes explain why a potential impact will not be significant. This principle follows from the nature of judicial review of agency action. As aptly explained by the First Circuit, “agency decisions must make sense to reviewing courts .... even in technical areas of regulation.” Puerto Rico Sun Oil Co. v. United States EPA 8 F.3d 73, 77 (1st Cir.1993). Courts must extend reasonable deference to NMFS’s determinations regarding the extent to which a circumstance affects listed species. NMFS pays for this deference with the obligation to actually make determinations on the record. It would be inconsistent with the court’s duty to assume that, in every BiOp, for every issue not discussed, NMFS considered the issue and found it insignificant. Moreover, when the record is silent as to the magnitude of an impact, the court cannot make the initial