We tested the hypothesis that piping plover (Charadrius melodus) habitat quality and chick survival on the Missouri River, USA, were lower on a cold-water reservoir and downstream from a hypolimnetic (cold-water) release dam with diel water fluctuations (Garrison Dam) than downstream from an epilimnetic dam (Gavins Point Dam). Plovers in adjacent alkali wetlands provided an index to the maximum reproductive potential in the region. Chicks gained weight more rapidly in the alkali wetlands than on epilimnetic and hypolimnetic river reaches. Invertebrate numbers and biomass were higher in the wetlands and epilimnetic reach, but chick survival was lower on the epilimnetic reach. Thus, piping plovers adapted to a variety of prey densities, and other factors, likely predation, reduced survival rates in the epilimnetic reach. Temporal and spatial variability in site quality indices suggests the need for a regional management strategy with different strategies at each site. Managers can minimize effects of local fluctuations in resource abundance and predators by ensuring protection of or creating geographically dispersed habitat.