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F. Protection of Endangered or Threatened Species and Their Habitat
Where a project adversely affects a species of fish, wildlife, or plant listed as threatened or endangered under the Endangered Species Act, the FWS or NMFS may establish reasonable and prudent alternatives (RPA) or measures (RPM). While FERC is not required to include such measures in the license, FERC and the licensee may be liable for damages if the license results in death, injury, or other harm to the listed species. As a practical matter, FERC treats RPA or RPM as mandatory conditions.
Under ESA section 7(a)(1), FERC, like any other federal agency, must protect and contribute to the recovery of all threatened and endangered species affected by their actions. Under ESA Section 3(3), FERC must “use… all methods and procedures which are necessary” for this purpose. Under ESA section 7(a)(2), FERC must, in consultation with FWS/NMFS, ensure that any action it authorizes, funds, or implements is not likely to jeopardize the continued existence of listed species or result in the destruction or adverse modification of designated critical habitat. In fulfilling this requirement, each agency must use the best scientific and commercial data available.
The ESA specifies special procedures for compliance with these mandates. Early in the licensing proceeding, FERC must determine whether its licensing action may affect listed species or critical habitat. Typically, the licensee will be designated as the non-federal representative for consultation and will prepare a Biological Assessment (BA) under FERC’s supervision. If, on receipt of the BA, FERC finds that the licensing action will not affect such species or habitat in the project area, and if NMFS/FWS concurs (in what is called a “concurrence letter”), then informal consultation ends.  Otherwise, FERC must initiate formal consultation – with NMFS with respect to marine wildlife or diadromous fish such as salmon, or the FWS regarding freshwater and terrestrial species such as bass or frogs. FWS/NMFS will review the information provided by FERC (including the BA), evaluate the status of the affected species, evaluate the possible direct, indirect, and cumulative impacts of the licensing action, and then prepare a Biological Opinion (BO) and Incidental Take Statement (ITS). The opinion must include: (1) supporting documentation, (2) discussion of the impacts of the action on listed species or critical habitat; and (3) FWS/NMFS’ opinion as to whether the action is likely to jeopardize the continued existence of a listed species.
If the FWS or NMFS, as appropriate, finds that the project may cause jeopardy to the listed species or adversely affect critical habitat, then the BO includes Reasonable and Prudent Alternatives (RPAs). These are alternatives that avoid jeopardy or adverse modification of critical habitat in a manner consistent with the intended purpose of the project, within the scope of FERC’s legal authority, and are economically and technologically feasible. If the agency finds that the project will not cause jeopardy or adverse modification to critical habitat, then the BO includes RPMs which minimize the impact of incidental take but do not modify the basic design, location, scope, duration, or timing of the Proposed Action. Finally, regardless of the type of BO, the ITS specifies the permissible level of take of the listed species.
Early in the proceeding, contact FWS/NMFS to learn whether federally listed species or critical habitat may exist in the project area.
If a species is threatened as a matter of fact but not yet listed for protection under the ESA, you should consider a corollary strategy of filing a petition to list the species. Such a petition should be filed in advance of the relicensing proceeding. See 16 U.S.C. § 1533(b); 50 C.F.R. § 424.14.
If the project may affect an already listed species, make a written request that FWS/NMFS include you in any discussions with the licensee regarding the conditions of the Biological Assessment or Opinion.
File comments on the Biological Assessment/Opinion both with that agency and FERC. As discussed above, you should ask the agency to include in the BO specific findings regarding the incidental take of listed species and impacts on critical habitat to establish accountability in the RPAs or RPMs. Thus, the agency may request that FERC reopen the license, by reinitiating consultation, if these measures do not achieve the required level of protection.
The ESA uses a different baseline for analysis of alternatives to protect and recover a listed species. The baseline does not include the licensed project, including past and continuing effects but does include other developments not subject to the ESA consultation.
 See 16 U.S.C. § 1536(b)(4), 50 C.F.R. §§ 402.02, 402.14(i)(1).
 16 U.S.C. § 1538.
 See 16 U.S.C. § 1538(a)(1)(B). Any person who knowingly violates ESA Section 9 may be assessed a civil penalty by FWS/NMFS of not more than $25,000 for each violation. See 16 U.S.C 1540(a)(1).
 See Tennessee Valley Authority v. Hill, 437 U.S. 153, 185 (1978). “One would be hard pressed to find a statutory provision whose terms were any plainer than those in § 7 of the Endangered Species Act. Its very words affirmatively command all federal agencies ‘to insure that actions authorized, funded, or carried out by them do not jeopardize the continued existence’ of an endangered species or ‘result in the destruction or modification of habitat of such species ….’” This language admits of no exception.” Id. at 173.
 Id., citing 16 U. S. C. § 1531(c), 1532(3) (emphasis added).
 “A Federal agency need not initiate formal consultation if, as a result of a biological assessment under § 402.12 . . . the Federal agency determines, with the written concurrence of [FWS or NMFS], that the proposed action is not likely to adversely affect any listed species or critical habitat.” 50 C.F.R. § 402.14(b)(1).
 See 50 C.F.R. § 402.01(b).
 See 50 C.F.R. § 402.14(i).
 To place a listed species in jeopardy is to “engage in an action that reasonable 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.” U.S. Fish and Wildlife Service, Endangered Species Glossary (2004), p. 3. Critical habitat is defined as:
“(i) the specific areas within the geographical area occupied by the species, at the time it is listed in accordance with the provisions of section 4 of this Act, on which are found those physical or biological features (I) essential to the conservation of the species and (II) which may require special management considerations or protection; or
(ii) specific areas outside the geographical area occupied by the species at the time it is listed in accordance with the provisions of section 4 of this Act, upon a determination by the Secretary that such areas are essential for the conservation of the species.”
16 U.S.C. § 1532(5)(A).
 See 50 C.F.R. § 402.02.
 See id.
 See id.
 See id.
 See 50 C.F.R. § 402.02 . The court in In re Operation of Missouri River System Litigation upheld FWS’ definition of baseline to include a “‘run-of-the-river’” baseline in which the dams and physical channel modifications are assumed to be in place, but all floodgates are assumed to be wide open, with no flow control. 421 F.3d 618, 632 (8th Cir. 2005).