Freshwater ecosystems are characterized by a high spatial complexity. This heterogeneity affects the distribution of aquatic organisms in riverine landscapes. Morphological variation in natural populations is driven by evolutionary forces. In crustaceans, morphological variations have been observed between different basins, environments, or developmental sequences along their geographical distribution. In this study, we assessed the possible effects of spatial scale on the phenotype of Aegla plana Buckup and Rossi, 1977 using geometric morphometrics. We examined 110 adult specimens from three river basins in southern Brazil. We used 13 morphological landmarks for the dorsal view of the carapace; the coordinates were superimposed using a generalized Procrustean analysis. We used a multivariate analysis to test the morphological variation in crabs from different basins, and we employed the Mantel test to assess the relationship of spatial and environmental factors with the principal components matrix for the carapace shape. Populations from different river basins differed significantly in carapace centroid size. Carapace shapes also differed significantly among the river-basin populations, and the interaction between sex and populations was also significant. The environmental and geographical matrices were correlated with the carapace shape matrix. This morphological variation shows an association with the geographical distribution of microbasins, which suggests a biogeographical effect on the distribution of A. plana.