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The Endangered Species Act (ESA) requires that the Corps of Engineers (Corps), in coordination with the appropriate resource agencies, will ensure that any action authorized, funded or carried out is not likely to jeopardize the continued existence of any federally listed threatened or endangered species or result in the destruction or adverse modification of critical habitat. On November 30, 2000, formal consultation between the U.S. Fish and Wildlife Service (USFWS) and the Corps under Section 7 of the ESA culminated with the "Biological Opinion on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project (BSNP), and Operation of the Kansas River Reservoir System" (BiOp). The 2000 BiOp concluded that the existing operation of Missouri River Main Stem System, the maintenance and operation of the BSNP, and operation of the Kansas Reservoir System jeopardizes the existence of the endangered interior least tern and pallid sturgeon and the threatened piping plover. It also concluded that there would be an incidental take of bald eagles.
On November 2,2003, the Corps submitted a Biological Assessment (BA) to the USFWS and requested reinitiation of formal consultation with the USFWS on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River BSNP, and Operation of the Kansas River Reservoir System. Reasons for submitting a new BA were based on new data on mortality of terns and plovers, the 2002 designation of critical habitat for the piping plover, and new information on Reasonable and Prudent Alternative (RPA) element I1 (Flow Enhancement). On November 10,2003, the USFWS accepted the new BA and started formal consultation. In the BA, the Corps accepted most elements from the RPA in the November 30,2000, BiOp but proposed replacing the element that required spring and summer flows. In addition, the Corps proposed a modified drought conservation plan, Gavins Point Dam summer releases, accelerated construction of shallow water habitat, pallid sturgeon hatchery improvements, accelerated pallid sturgeon brood stock collection, and adaptive management (including research, monitoring and evaluation, and flow tests).