The annual flood pulse in tropical lowland rivers creates a continually moving land–water margin that forces aquatic organisms of the littoral zone to relocate to new habitats at intervals ranging from days to weeks. Thus, species assemblages in patchy littoral-zone habitats have large potential to be influenced by stochastic colonization dynamics, whereby organisms may exhibit weak selection for mesohabitat features and arrive on a patch in no particular sequence. We examined species assemblages of fishes and macroinvertebrates occupying habitats of varying structural complexity through an annual flood cycle of the Cinaruco River, a species-rich floodplain river in the southern llanos of Venezuela. We collected 268 standardized samples that contained 54,596 individual fishes representing 156 species (23 families) and 6973 macroinvertebrates representing 8 families. Analysis of species-specific patterns of habitat occupancy based on a randomization procedure indicated greater species selectivity during low water (92% of taxa) relative to rising- and falling-water periods (60% and 63% of taxa, respectively). Community-wide correspondence analysis (CA) revealed similar patterns. Assemblages from similar habitat types clustered together in the CA ordination, and these nonrandom patterns were most apparent during low water. Results from partial canonical correspondence analysis revealed that assemblage structure was strongly influenced by habitat type (patches of different composition located within the shallow littoral zone of either the river main channel or lagoons), which accounted for 56% of the total explainable variation in the species × sample matrix. Mesohabitat parameters (e.g., water velocity, depth), sampling period (month), and location on the landscape explained 30%, 23%, and 17% of variation, respectively. As water level changes and the aquatic–terrestrial interface moves across the landscape, species assemblages in patchy littoral habitats, while highly variable, reconstitute with significant determinism. At the same time, a large proportion of unexplained variation in assemblage structure probably is associated with unmeasured components of landscape variation as well as a stochastic element in colonization dynamics.