We document patterns of fruit and vertebrate abundance within an extensive, virtually undisturbed mosaic of seasonally flooded (várzea and igapó) and unflooded (terra firme) forests of central Amazonia. Using phenological surveys and a standardised series of line-transect censuses we investigate the spatial and temporal patterns of immature and mature fruit availability and how this may affect patterns of habitat use by vertebrates in the landscape. All habitats showed marked peaks in fruiting activity, and vertebrate detection rates varied over time for most species both within and between forest types. Many arboreal and terrestrial vertebrates used both types of flooded forest on a seasonal basis, and fluctuations in the abundance of terrestrial species in várzea forest were correlated with fruit availability. Similarly, the abundance of arboreal seed predators such as buffy saki monkeys (Pithecia albicans) and macaws (Ara spp.) were closely linked with immature fruit availability in terra firme forest. We conclude that highly heterogeneous landscapes consisting of terra firme, várzea and igapó forest appear to play an important role in the dynamics of many vertebrate species in lowland Amazonia, but the extent to which different forest types are used is highly variable in both space and time.