Environmental and commercial fishing organizations^[1] (collectively "American Rivers"), appeal the district court's denial of their motion for summary judgment and its grant of defendants' cross-motion for summary judgment. The defendants are the National Marine Fisheries Service ("NMFS") and the federal agencies^[2] that operate the Federal Columbia River Power System ("River Power System"). American Rivers contends that the federal agencies violated § 7(a)(2) of the Endangered Species Act, 16 U.S.C. § 1536(a)(2), because the operation of the River Power System jeopardizes the existence of the Snake River salmon and adversely modifies the salmon's critical habitat. Specifically, American Rivers challenges the federal agencies' decision to use transportation measures-moving juvenile salmon downstream in trucks and barges-to avoid a determination that the operation of the River Power System jeopardizes the existence of the salmon.

"Salmon and hydropower are the two great natural resources of the Columbia River Basin." Northwest Resource Info. Ctr., Inc. v. Northwest Power Planning Council, 35 F.3d 1371, 1375 (9th Cir.1994), cert. denied, --- U.S. ----, 116 S.Ct. 50, 133 L.Ed.2d 15 (1995) (hereinafter Northwest Power ). The present case involves the continuing conflict between these two important resources.

Snake River sockeye and chinook salmon are anadromous fish--they hatch and spend their first years in fresh water, reach mature size while rearing in the Pacific Ocean, and return to their natal streams and lakes to spawn and die. Anadromous fish runs in the Columbia River Basin have dwindled as a result of human activities since the European settlement of the Northwest. Northwest Power, 35 F.3d at 1376. The decline of these stocks of salmon has been caused by over-harvest, habitat degradation, predation, poor ocean rearing conditions, and the construction and operation of over 200 dams in the Columbia River Basin. 57 Fed.Reg. 14,654, 14,660, 14,661.

In 1991, National Marine Fisheries Service listed the Snake River sockeye salmon as an endangered species. 56 Fed.Reg. 58,619. The following year, NMFS listed the Snake River spring/summer and fall chinook^[3] as threatened species. 57 Fed.Reg. 14,653-54. On December 28, 1993, NMFS designated the critical habitat^[4] for these three species, which encompasses the Snake River and Columbia River migratory corridor. 58 Fed.Reg. 68,544. Despite the salmon's listed^[5] status, only one Snake River sockeye returned to spawn in the Snake River in 1994. In 1995, only 1,800 Snake River spring/summer chinook and 350 Snake River fall chinook returned to the river to spawn. These numbers demonstrate that the listed salmon continue their march toward extinction.

The present controversy between salmon and hydropower concerns the downstream migration of juvenile salmon or "smolts" in the Columbia River Basin. Once the salmon hatch in the upstream areas of the Columbia River Basin, the smolts travel downstream to the Pacific Ocean. During this downstream migration the smolts pass eight of the dams and reservoirs that are part of the River Power System. The Bureau of Reclamation and the Corps of Engineers operate these hydroelectric, flood control, and water storage projects. The importance and magnitude of the River Power System is demonstrated by the fact that it generates approximately half of the electricity used in the Pacific Northwest.

All parties agree that the existence of the River Power System impedes the migration of salmon. At present, there are four ways in which the salmon migrating downstream may pass the eight mainstream Columbia and Snake River hydroelectric projects. The salmon may: (1) spill over the dams; (2) pass through the power turbines; (3) bypass to transportation facilities, including barges or trucks; or (4) bypass back into the river. Idaho Dep't of Fish & Game v. National Marine Fisheries Serv., 850 F.Supp. 886, 889 n. 5 (D.Or.1994), vacated as moot, 56 F.3d 1071 (9th Cir.1995). Each of these methods is subject to scientific debate as to its effectiveness and benefit to the listed salmon. See Northwest Resource Information Center, Inc. v. National Marine Fisheries Serv. (hereinafter National Marine ), 56 F.3d 1060, 1063-64 (9th Cir.1995) (discussing the mechanics and relative benefits of each method).

Regardless of how the smolts pass the dams, the operation of the River Power System causes mortality to the smolts during their downstream migrations. The dams reduce water flow through reservoirs which slows the salmon's passage and contributes to salmon mortality. The salmon's slow passage through these reservoirs increases the exposure time of the juvenile salmon to: (1) predation; (2) higher water temperatures which make the salmon more susceptible to disease; and (3) water quality problems including dissolved gas supersaturation which causes gas bubble disease in juvenile and adult salmon. Moreover, during downstream migration some of the smolts pass through the hydroelectric turbines and emerge injured or disoriented, rendering them easy prey for squawfish. Furthermore, smolts that are diverted through the bypass systems at the dams may suffer descaling, disorientation, and stress.

The gravity of the salmon mortality problem is illustrated by NMFS's own estimate of cumulative passage mortality, which was as high as ninety-one percent for spring/summer chinook passing the mainstream hydroelectric projects. Salmon passage mortality through the River Power System can conceptually be divided into: (1) natural mortality; (2) additional mortality due to the existence of the River Power System; (3) additional mortality that varies with the operation of the River Power System; and (4) additional mortality from other human activities. However, the extent of the smolt mortality that is a direct result of the operation of the River Power System is unknown.

In 1968, NMFS first experimented with transportation as a means of facilitating the smolts downstream migration. Snake River smolts have been transported from Lower Granite, Little Goose, and McNary Dams since the 1970s and from Lower Monumental Dam since 1993. Today the smolt transportation program entails removing the migrating juvenile salmon from the river, transporting them around the dams, and then releasing them back into the Columbia River below Bonneville Dam to continue their journey to the Pacific Ocean.

The Corps of Engineers operates the transportation program during the juvenile migration season.^[6] All four dams involved in the transportation program have mechanical bypass systems that divert a portion of the juvenile salmon away from the power house turbines and into vertical gatewells. From the gatewells, the salmon pass through small orifices into bypass channels which run the length of the power house. The salmon then enter a primary dewatering facility, and then a high velocity pipe or flume that carries them to the transportation facility where they are separated, sorted, marked, and examined. The salmon then are held in raceways and from these raceways they are loaded into tanker trucks or barges. The transportation barges are specially equipped to circulate river water into the holding tank. It takes approximately forty hours for a barge to travel to the release site below the Bonneville Dam. Once the salmon are released, they continue their migration for another 140 miles to the Pacific Ocean.

As with the other methods of passage around the dams, transportation also causes mortality. American Rivers contends that transportation results in the following negative impacts on the juvenile salmon: (1) stress and physical injury which accompanies bypass and handling; (2) predation and disease transmission during holding and transport; (3) predation at the point of release; and (4) homing impairment of returning adults. At this point in time, scientific research is inconclusive regarding the ability of the transportation program to improve the survival of the salmon. Although the efficacy of the transportation program has been questioned, scientific evidence suggests that it is more probable than not that transportation improves the relative survival of juvenile salmon under certain hydroelectric operational scenarios and flow regimes.

The Endangered Species Act ("ESA"), 16 U.S.C. §§ 1531-1543, has both substantive and procedural provisions designed to protect endangered species and their habitat. These provisions are triggered when a species is listed as endangered or threatened. 16 U.S.C. § 1533. Section 7(a)(2) of the ESA requires federal agencies 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...." 16 U.S.C. § 1536(a)(2). If a contemplated agency action may affect a listed species, then the agency must consult with the Secretary of the Interior,^[7] either formally or informally. 50 C.F.R. § 402.14(a); 16 U.S.C. § 1536(a)(4). The agency first prepares a biological assessment, in which it evaluates the potential effects of an action on the listed species and its critical habitat. 50 C.F.R. § 402.12(a). If the agency discovers that its action may affect a listed species or its critical habitat, the agency must initiate formal consultation with NMFS. 50 C.F.R. § 402.14(a). In formal consultation, NMFS must prepare a biological opinion evaluating the effects of the action. NMFS determines whether the action will jeopardize a listed species. 16 U.S.C. § 1536(b)(3)(A); 50 C.F.R. § 402.14(h)(3). If NMFS makes a jeopardy finding, then it may also suggest reasonable and prudent alternatives to the proposed action. Id. By definition, the reasonable and prudent alternatives may not jeopardize the listed species or result in the destruction or adverse modification of its critical habitat. Id.

A discussion of the chronology of events and the succession of biological opinions^[8] is necessary to understand the disposition of this case.

On December 2, 1993, the Corps of Engineers, the Bureau of Reclamation, and the Bonneville Power Administration forwarded a biological assessment to NMFS with a request for consultation on the 1994-1998 operation of the River Power System. On March 16, 1994, NMFS issued a biological opinion ("1994-1998 Biological Opinion") that concluded the 1994-1998 River Power System operations would neither jeopardize the Snake River salmon nor adversely modify designated critical habitat.

At the time the 1994-1998 Biological Opinion was issued, a lawsuit was pending in Oregon district court regarding the 1993 Biological Opinion for the operation of the River Power System. On March 28, 1994, the district court decided that the 1993 Biological Opinion was arbitrary and capricious. Idaho Dep't of Fish & Game v. National Marine Fisheries Serv., 850 F.Supp. 886, 900 (D.Or.1994), vacated as moot, 56 F.3d 1071 (9th Cir.1995). As a result of the district court's holding, the federal agencies reinitiated consultation on the River Power System. However, the 1993 Biological Opinion was about to expire and the legal errors in the 1993 Biological Opinion were carried over into the 1994-1998 Biological Opinion (which had just been issued on March 16, 1994). Thus, the federal agencies reinitiated consultation on the 1994-1998 Biological Opinion, instead of the 1993 Biological Opinion. See Idaho Dep't of Fish & Game v. National Marine Fisheries Serv., 56 F.3d 1071, 1074 (9th Cir.1995).

On August 4, 1994, American Rivers filed suit against the Corps of Engineers, the Bureau of Reclamation, and the National Marine Fisheries Service.^[9] The plaintiffs alleged that the 1994-1998 Biological Opinion violated § 7(a)(2) of the ESA.^[10] Specifically, American Rivers contended that the federal defendants violated the ESA by relying on the transportation of Snake River smolts to conclude that the 1994-1998 operations of the River Power System are unlikely to jeopardize the continued existence of the listed salmon.

On October 21, 1994, the defendants moved for a stay in the proceedings to reinitiate consultation on the 1994-1998 Biological Opinion and bring the opinion into compliance with the district court's order in Idaho Dep't of Fish & Game. On November 18, 1994, American Rivers moved for summary judgment. Soon thereafter, the district court granted the defendants' motion to stay the proceedings until February 1, 1995.

On March 2, 1995, NMFS issued a new biological opinion ("1995 Biological Opinion") which superseded the 1994-1998 Biological Opinion. In contrast to the prior biological opinion, the 1995 Biological Opinion concludes that the operation of the River Power System would jeopardize the continued existence of the listed salmon and adversely modify their critical habitat. However, the 1995 Biological Opinion recommends a reasonable and prudent alternative for the operation of the River Power System.^[11] The reasonable and prudent alternative relies on smolt transportation as a major means of mitigating the adverse impacts of the River Power System. However, fewer listed salmon would be transported under the 1995 Biological Opinion with its reasonable and prudent alternative than would have been transported under the 1994-1998 Biological Opinion.

On March 10, 1995, the Corps of Engineers and the Bureau of Reclamation formally adopted the 1995 Biological Opinion, with its reasonable and prudent alternative. On March 15, 1995, the federal defendants filed a cross-motion for summary judgment in which they argued, inter alia, that American Rivers' claims were mooted by the issuance and adoption of the 1995 Biological Opinion. The district court held American Rivers' claims were not moot and granted the defendants' motion for summary judgment.

This case presents two threshold questions which must be decided before we address the merits. First, was American Rivers' challenge to the 1994-1998 Biological Opinion rendered moot by the issuance of the 1995 Biological Opinion? Second, is American Rivers precluded from challenging the 1995 Biological Opinion because they did not file a timely 60-day notice of intent to sue prior to initiating this action? We address these questions in turn.

The defendants contend that American Rivers' challenge to the 1994-1998 Biological Opinion is moot because the 1995 Biological Opinion replaced the 1994-1998 Biological Opinion.^[12]

A federal court's jurisdiction is limited to cases or controversies. U.S. Const. art. III, § 2; Powell v. McCormack, 395 U.S. 486, 496 n. 7, 89 S.Ct. 1944, 1950 n. 7, 23 L.Ed.2d 491 (1969). A claim is moot if it has lost its character as a present, live controversy. American Tunaboat Ass'n v. Brown, 67 F.3d 1404, 1407 (9th Cir.1995). A federal court does not have jurisdiction "to give opinions upon moot questions or abstract propositions, or to declare principles or rules of law which cannot affect the matter in issue in the case before it." Church of Scientology v. United States, 506 U.S. 9, 12, 113 S.Ct. 447, 449, 121 L.Ed.2d 313 (1992) (citations omitted). If an event occurs that prevents the court from granting effective relief, the claim is moot and must be dismissed. GTE California, Inc. v. FCC, 39 F.3d 940, 945 (9th Cir.1994); National Marine, 56 F.3d at 1069.

Issues which are "capable of repetition, yet evading review" present an exception to the mootness doctrine. Southern Pac. Terminal Co. v. Interstate Commerce Comm'n, 219 U.S. 498, 515, 31 S.Ct. 279, 283, 55 L.Ed. 310 (1911); Alaska Fish & Wildlife Fed'n v. Dunkle, 829 F.2d 933, 939 (9th Cir.1987), cert. denied, 485 U.S. 988, 108 S.Ct. 1290, 99 L.Ed.2d 501 (1988). "The doctrine is limited to extraordinary cases in which: (1) the duration of the challenged action is too short to be fully litigated before it ceases; and (2) there is a reasonable expectation that the plaintiffs will be subjected to the same action again." Dunkle, 829 F.2d at 939 (citation omitted); see also Native Americans for Enola v. U.S. Forest Serv., 60 F.3d 645, 646 (9th Cir.1995).

In Idaho Dep't of Fish & Game v. National Marine Fisheries Serv., 56 F.3d 1071 (9th Cir.1995), we addressed the issue of mootness in a case which involved some of the same underlying facts as those in the present case. In Idaho Dep't of Fish & Game, NMFS appealed the district court's determination that the 1993 Biological Opinion was arbitrary and capricious. Id. at 1074. This court then held that the issuance of the 1995 Biological Opinion mooted the challenge to the 1993 Biological Opinion. Id. at 1075. Furthermore, we concluded the case did not fit the "capable of repetition, yet evading review" exception to the mootness doctrine because the 1995 Biological Opinion would not evade review. Id. We relied on the fact that the 1995 Biological Opinion spanned a period of four years, 1994-1998,^[13] and thus there was still time to litigate the agency decisions made pursuant to the 1995 Biological Opinion. Id.; see also Aluminum Co. of America v. Bonneville Power Admin., 56 F.3d 1075, 1077 (9th Cir.1995) (holding that a challenge to 1993 Biological Opinion for operations of the River Power System is moot).

The case at bar is not distinguishable from Idaho Dep't of Fish & Game, 56 F.3d 1071 (9th Cir.1995). Both cases are challenges to biological opinions on the operations of the River Power System. The only difference is that the present case began as an attack on the 1994-1998 Biological Opinion, while Idaho Dep't of Fish & Game was a challenge to the 1993 Biological Opinion. This difference is of no consequence. As in Idaho Dep't of Fish & Game, the biological opinion in the present case has been superseded by the 1995 Biological Opinion. Therefore, any challenge to the 1994-1998 Biological Opinion is moot.

Furthermore, American Rivers' challenge to the 1994-1998 Biological Opinion will not evade review because the 1995 Biological Opinion will not expire until 1998. Accordingly, we dismiss the challenge to the 1994-1998 Biological Opinion as moot. Moreover, because the 1995 Biological Opinion was issued before the district court granted defendants' summary judgment motion, any challenge to the 1994-1998 Biological Opinion was moot below.

Section 11(g) of the Endangered Species Act permits citizens to sue to enforce compliance with the Act. 16 U.S.C. § 1540(g). However, before a citizen can file an action, the citizen must give the Secretary of the Interior and any alleged violators written notice of intent to sue sixty days prior to filing suit. 16 U.S.C. § 1540(g)(2)(A)(i). This requirement is jurisdictional. Save the Yaak Comm. v. Block, 840 F.2d 714, 721 (9th Cir.1988).

However, after oral argument in this case, the Supreme Court decided Bennett v. Spear, --- U.S. ----, 117 S.Ct. 1154, 137 L.Ed.2d 281 (1997). In Bennett, the Court held that challenges to the adequacy of biological opinions against the Secretary of the Interior, when acting in his capacity as Administrator of the Endangered Species Act, are not properly pled as citizen suit claims under Section 11(g)(1)(A) of the Act. The Court then held that such claims could be pled under the Adminstrative Procedure Act, which authorizes courts to set aside agency actions found to be "arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law." 5 U.S.C. § 706.

Such actions under the Administrative Procedure Act do not require the sixty-day notice requirement set forth in the Endangered Species Act. Therefore, failure to provide such notice does not deprive the court of jurisdiction to entertain such claims.

The Administrative Procedure Act may be brought only to challenge final agency actions. 5 U.S.C. § 704. The Supreme Court in Bennett set forth a two-part test for determining whether an agency action was final for the purposes of the Administrative Procedure Act: (1) the action had to mark the consummation of the agency's decisionmaking process; and (2) the action had to be one from where rights or obligations have been determined or from where legal consequences will flow. --- U.S. at ----, 117 S.Ct. at 1168.

In this case, the biological opinion was a jeopardy opinion with alternatives and included a statement which permitted the agency to "take" the endangered or threatened species under certain terms and conditions. The biological opinion in this case was similar to the one in Bennett and therefore American Rivers properly pled Administrative Procedure Act claims against the Northern Maine Fisheries Service. Administrative Procedure Act claims were not pleaded against the Corps of Engineers and the Bureau of Reclamation. The claims against those agencies for violations of the Endangered Species Act remain subject to the Act's sixty-day notice requirement and therefore should be dismissed.

As to the 1995 Biological Opinion, we REMAND this case for further proceedings on American Rivers' Administrative Procedure Act claim against the National Marine Fisheries Service. We further REMAND to dismiss the Endangered Species Act claim against the Corps of Engineers and the Bureau of Reclamation for the failure to give the sixty-day notice.