Consideration of annual population count data, stream flows, water levels, and nesting habitat availability over a 29-year period suggest that Least Terns (Sternula antillarum athalossos) nesting along the Cheyenne River and Oahe Reservoir in South Dakota, USA, select areas primarily in response to reservoir water levels early in the breeding season. Generalized linear models were selected in an information-theoretic framework and showed important relationships between adult Least Tern numbers and reservoir levels, as well as a negative long-term temporal trend in both survey areas. Reservoir levels alone could not account for the temporal trend. The number of adult Least Terns on the Cheyenne River was positively correlated (R = 0.668) with mean May reservoir water levels—a more important relationship than that between adult numbers and river levels. The number of adults on the Oahe Reservoir was negatively correlated (R = -0.573) with mean May reservoir water levels. Numbers of adults on the Cheyenne River and on Oahe Reservoir were negatively correlated (R = -0.684), suggesting that birds may interact as one population across the two areas. This information should help managers to consider ecological relationships among segments of the Least Tern population on the Missouri River and its tributaries and options for managing Least Terns on the Cheyenne River, Oahe Reservoir, and elsewhere on the Missouri River system.