Natural variation in flow conditions is hypothesized as a primary driver of population variation in stream biota, including benthic fishes. We conducted annual fish surveys at ten shoals on the Etowah River, Georgia, 1998-2006, to monitor rare and imperiled species and examine species-specific responses to interannual variation in spring and summer flow conditions. Survey data were used to assess how the probability of occurrence of adult and young-of-year fishes in any seine-set was influenced by antecedent flow conditions and habitat. We used hierarchical logistic regression to model factors at multiple levels thought to influence the occurrence of ten species from three families, Cyprinidae, Ictaluridae, and Percidae. Microhabitat features (e.g., presence of Podostemum) were the strongest predictors of species occurrence in a seine-set. Antecedent flow conditions also influenced the probability of species occurrence. Increasing days of high summer flow (days exceeding one standard deviation over the long-term average) reduced the probability of occurrence of young-of-year of most species during fall surveys. These findings suggest the need for stable summer flows in warmwater rivers to allow for strong species recruitment, with implications for the management of regulated rivers and possible response of benthic fishes to climate change predictions for the southeastern U.S.