A long-term investigation (1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006) was conducted on the relation between Yellowstone and Missouri River discharges, water level (elevation) changes of Lake Sakakawea, a Missouri River mainstem reservoir in western North Dakota, and the ecology of the Yellowstone-Sakakawea stock of paddlefish Polyodon spathula, a zooplanktivorous Acipenseriform fish. After impoundment in December 1953, Lake Sakakawea filled gradually over a 13-year period (1953-1966). Water levels were lowered sharply and briefly in 1977 and 1981 and for much more prolonged periods of 1988-1993 and 2000-2006 associated with drought conditions in the central United States and water management decisions by the U.S. Army Corps of Engineers.The 1995 year class of paddlefish, by far the strongest in the 16-year study period, was associated with the sharp rise in water level from August 1993 through 1995, the longest continuous rise since the initial filling and the only period since initial filling when reservoir levels rose substantially in three consecutive years. High reservoir levels were associated with higher densities of zooplankton (all taxa combined and Leptodora kindtii, the primary food of age 0 paddlefish), stronger year classes (based on counts of age 0 fish along standard transects), greater mean weight and condition of age 0 fish in August, greater mean weights of recruits, higher growth rate of adult fish, and greater weight of gonadal fat bodies (GFBs), an indicator of energy storage, in absolute weight, as a percentage of gonad weight, and as a percentage of fish weight. Sixty-three percent of the variation in the ratio of GFB weight/gonad weight was explained by reservoir level. Fish tagged as adult migrants and recaptured in succeeding years after rearing in rising and high reservoir conditions gained an average of 0.04 kg/yr, whereas fish rearing in falling-and low-reservoir conditions lost an average of 0.19 kg/yr. Missouri River discharge during spring was significantly correlated with estimated age 0 year class strength, but a similar relationship did not hold for the Yellowstone River, which is the river used by most spawning paddlefish. Results of this study are consistent with studies from Lake Sakakawea and other reservoirs indicating that trophic upsurge in recently filled (and refilled) reservoirs favors the development of stronger year classes, faster growth, better condition, and larger size at maturity of fishes. Higher riverine discharges, thought to favor paddlefish reproductive success, were also typically associated with a rising or high reservoir. In contrast, low-reservoir levels over the period [2000][2001][2002][2003][2004][2005][2006] have negatively affected paddlefish year class strength, growth, and energy storage. If, in succeeding years, Lake Sakakawea once again is allowed to rise to full pool as it did over the period 1993-1995, inundation of the shorelines and the vegetation can be expected to result in another ups...