Variations in environmental conditions along gradients play an important role in species distribution through environmental filtering of morphological and physiological traits; however, their effects on bat diversity remain poorly understood. Here, we investigate the effect of the distance to the nearest watercourse, terrain elevation, vegetation clutter, basal area and canopy height on taxonomic, functional and phylogenetic diversity and on the predominance of some functional traits (body mass, wing morphology and trophic level) of bat assemblages (phyllostomid and mormoopid bats) in a terra firme forest, in the northeastern Brazilian Amazon. We captured bats using mist nets in 15 permanent plots over a 25 km2 area of continuous forest. We captured 279 individuals belonging to 28 species with a total of 77.760 m2.h of sampling effort. Our results showed that bat richness increases as a function of distance to the nearest watercourse and that the assemblage also changes, with more diverse taxonomic and functional groups in areas further from the watercourse. Furthermore, elevation positively affects species richness, and the basal area of the forest positively influences the average body mass of bats. Taken together, our results demonstrate that subtle variations in the environmental conditions along a local scale gradient impact on the main dimensions of bat diversity in primary forests.