In tropical floodplain rivers, communities associated with structurally complex habitats are disassembled and reassembled as aquatic organisms repeatedly colonize new areas in response to gradual but continuous changes in water level. Thus, a neutral model reflecting random colonization and extinction dynamics may be sufficient to predict assemblage patterns at the scale of local habitat patches. If water level fluctuations and associated patch dynamics are sufficiently predictable, however, community assembly on habitat patches also may be influenced by species-specific responses to habitat features and/or species interactions. We experimentally manipulated structural complexity and proximity to source habitat (which influences colonization rate) of simulated rocky patches in the littoral zone of a tropical lowland river and demonstrate significant effects of both factors on species density of fishes and macroinvertebrates. Interspecific variation in vagility significantly affected assemblage response to habitat complexity. In a second experiment, created habitat patches were sampled over time intervals ranging from 1 day to 36 days to examine temporal dynamics of community assembly. A null-model test revealed that assemblage structure became increasingly non-random, concomitant with increasing species density, over time. Community dynamics in newly formed habitat patches appeared to be dominated by dispersal, whereas in older patches, abundances of individual species increasingly were influenced by habitat characteristics. These data suggest that species-specific responses to environmental variation resulted, in part, because of species interactions. We conclude that community assembly in shallow habitats of this tropical lowland river is influenced by physical habitat characteristics, the spatial distribution of habitat patches, and species interactions as habitats are saturated with individuals.