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Final Report September 2000 EXECUTIVE SUMMARY The Green River system of the upper Colorado River basin in Utah and Colorado supports populations of three endangered fishes - humpback chub Gila cypha, Colorado pikeminnow Ptychocheilus lucius, and razorback sucker Xyrauchen texanus - and it historically supported the endangered bonytail Gila elegans. Bonytails are almost unknown in recent collections. Razorback suckers are extremely rare and continue to decline. Humpback chubs and Colorado pikeminnow still reproduce and recruit in the Green River system, but their long-term viability in the system is uncertain. Systemwide reductions in spatial and temporal components of habitat complexity, attributed to past and ongoing alterations in river flow and temperature, have been implicated as major factors contributing to the decline of all the endangered fishes. Operation of Flaming Gorge Dam, which is located on the upper main-stem Green River, strongly influences downstream flow and temperature regimes and the ecology of riverine biota, including native fishes. The U.S. Fish and Wildlife Service (Service), in its 1992 Biological Opinion on Operation of Flaming Gorge Dam (Biological Opinion), concluded that continuation of historic operations at Flaming Gorge Dam was likely to further reduce the distribution and abundance of these federally protected species and thus jeopardize their continued existence. The Biological Opinion identified a reasonable and prudent alternative containing several related elements. These elements included (1) refine the operation of Flaming Gorge Dam so that flow and temperature regimes more closely approximate historic conditions; (2) conduct a 5-year research program ("Flaming Gorge Flow Recommendations Investigation") to include implementation of winter and spring"research flows" beginning in 1992, to allow for potential refinement of flows for those seasons; (3) determine the feasibility and effects of releasing warmer water during the late spring through summer period and investigate the feasibility of retrofitting river bypass tubes to include power generation capability, thereby facilitating higher spring releases; (4) legally protect Green River flows from Flaming Gorge Dam to Lake Powell; and (5) initiate discussions with the Service after conclusion of the Flaming Gorge Flow Recommendations Investigation to examine further refinement of flows and temperatures for the endangered fishes. The Flaming Gorge Flow Recommendations Investigation, which began in 1992 but also included research conducted in 1990 and 1991 (while the Biological Opinion was being prepared), was conducted under the auspices of the Upper Colorado River Endangered Fish Recovery Program. The purpose of the investigation was to evaluate and refine the original flow and temperature recommendations given in the Biological Opinion as part of the reasonable and prudent alternative. Specifically, the Flaming Gorge Flow Recommendations Investigation was intended to determine the biological and physical responses of the Green River system to seasonal flow modifications, develop data for refinement of flow recommendations, and investigate the potential effects of increasing the temperature of water released from Flaming Gorge Dam. Specific objectives of the investigation were to (1) track reproduction of the endangered fishes and determine relationships among seasonal flows, water temperatures, and xxiii