In Neotropical forests fruits are key resources for a great diversity of vertebrates, including many frugivorous bats, but little is known about the factors that determine their availability. We studied forest inundation and river banks as determinants of the spatial variation in the availability of fruits for bats in lowland Amazonia. We sampled the bat assemblage composition, fruit availability, and bat diet in terra firme upland forest and in two types of flooded forest — várzea and igapó. Two distinct frugivore bat guilds were found in both terra firme and flooded forests: (1) canopy frugivores, feeding mainly on Ficus and Cecropia, and (2) understorey frugivores that feed mainly on Vismia and Piper. Fruits consumed by the canopy guild were more abundant in the flooded forests — particularly in the nutrient-rich várzea, but those dominating the understory guild diet were most abundant in terra firme. Availability of both fruit genera most consumed by the canopy guild was greater along river banks than in the forest matrix. For the understory guild, the greater abundance of Vismia along river banks was compensated for by a higher availability of Piper in the matrix. In conclusion, both factors influence the availability of fruits, although differently for the canopy and understory guilds. The resulting differences in fruit abundance may explain variations in bat assemblages of the different forest types. River banks play a particularly important role in providing food for bats of both guilds, but are under particularly heavy human pressure.