The causes of fish community organization in a system of habitat patches with different environmental conditions were described using a data set of 65 sites sampled during the dry season. Incorporating the patchy heterogeneous structure, variation partitioning allowed us to specifically evaluate the fine-scale neutral processes produced by spatial autocorrelation within habitat patches, and the broad-scale dispersal limitations between patches. Only the second subset of spatial variables was significant; dispersal limitation was relatively low between habitat patches of varzea lakes. An analysis of functional ecology allowed an empirical description of the functional mechanisms of alpha and beta niche differentiation, and an assessment of the phylogenetic signal. The trait-convergence assembly pattern among habitat patches indicated that fish in turbid river channels were better adapted to low light than fish in transparent black and clear water bodies. Also, fish in varzea lakes had a wider ecological range; this association indicated phylogenetic niche conservatism. The trait-divergence assembly pattern was almost expressed by body weight and was prominent in varzea lakes; combined with ecological range and sensory adaptation, this association indicated a marginal phylogenetic signal. These results suggest the radiation of species-rich clades with a high degree of sensory adaptation may have occurred in the seasonal environment of varzea lakes. This resulted in larger ecological distribution and innovative life histories tightly synchronized with periodic flooding. The lineage-specific sensory adaptation and subsequent landscape and evolutional history of habitat specialization were also found to actually contribute to the fish metacommunity dynamic in the Bolivian Amazonian lowland.