1. River system dynamics results in ecological heterogeneities that play a central role in maintaining biodiversity in riverine regions. In central Amazonia, large expanses of forest are seasonally flooded by nutrient-rich water (várzea forests) or by nutrient-poor water (igapó forests). Inundation patterns and the nutrient load of floodwaters are perhaps the most important abiotic factors determining spatial ecological variations in lowland Amazonia, and so they are expected to strongly influence the structuring of animal communities. 2. We examined how inundation patterns and water-nutrient load influence the structure of neotropical assemblages of bats, one of the most diverse vertebrate groups in tropical forests. Bat assemblages were sampled with mist nets in central Brazilian Amazonia, across a mosaic of várzea, igapó, and non-flooding nutrient-poor terra firme forests in the low- and high-water seasons. 3. An ordination analysis clearly separated the assemblages of the three forest types, demonstrating the structural relevance of both flooding and floodwater-nutrient load. Flooded forests had lower species richness because of the absence or rarity of species that make roosts out of leaves of understorey plants, and of those that feed on fruits of shrubs. Gleaning insectivores, also partly dependent on the understorey, were less abundant in flooded forests, but aerial insectivores more abundant, presumably because they benefited from a less cluttered foraging environment. These differences suggest that flooding affects bat assemblages mostly because it reduces the availability of niches associated with understorey vegetation, which tends to be sparser in flooded forests. 4. Nutrient-rich várzea forests had a bat biomass twice that of nutrient-poor igapó and unflooded forests. This difference was not only mostly due to a greater overall abundance of bats, but also attributable to a disproportionate higher abundance of large-bodied bat species. 5. We concluded that both flooding and floodwater-nutrient load are very important in the structuring of lowland Amazonian bat assemblages, with inundation mostly constraining the species composition of the assemblages, and water-nutrient load mostly influencing the abundance of species. The distinctiveness of bat assemblages associated with flooding emphasizes the need to preserve inundated forests, which are under particular pressure in Amazonia.