Habitat size and heterogeneity are among the main factors determining local species richness. However, distinguishing between them is critical to discriminate stochastic from the habitat-driven processes underlying local patterns of species distribution. Here, we test the individual effects and interaction of habitat size and heterogeneity in driving the occurrence of species in water bodies in the Brazilian Caatinga dry forest. We surveyed sites of different sizes and degrees of physical heterogeneity (i.e., margin architecture and plant stratification) and performed univariate and multivariate analyses to test the effect of these factors on species richness and composition. We found a clear habitat size effect but a negligible influence of habitat heterogeneity on the species richness at breeding sites. Specific habitat features may be important for few species, however. Our findings suggest an overall stochastic usage of water bodies by the anurans in the Caatinga and highlight the need of distinguishing the effects of habitat availability from those of habitat heterogeneity when investigating the structure of anuran assemblages.