In this study, patterns of spatial synchrony in population fluctuations (cross-correlation) of an endemic fish assemblage of a Neotropical reservoir (Segredo Reservoir, Iguaçu River, Paraná State, Brazil) were reported. First, the level of population synchrony for 20 species was estimated. Second, population synchrony was correlated, using the Mantel test, with geographical distances among sites (n = 11) and also environmental synchrony (temperature). Nine species presented significant correlations between spatial synchrony and geographic distances (Astyanax sp. b, Astyanax sp. c, Pimelodus sp., Hoplias malabaricus, Crenicichla iguassuensis, Hypostomus derbyi, Hypostomus myersi, Rhamdia branneri, and R. voulezi). Considering the ecology of the species and the significant relationship between population and environmental synchronies, it seems that environmental stochasticity is the most plausible hypothesis in explaining the observed synchrony patterns.