Wet-season flooding causes dietary shifts in tropical freshwater fish by regulating instream productivity, habitat structure and food availability. These dynamics have been comprehensively documented worldwide, but data are limited for Australia’s Wet Tropics rivers. The aim of the present study was to extend our earlier fish–habitat model for these systems by examining the role of trophic dynamics in determining fish assemblage composition. Chlorophyll a and phaeophytin concentrations, benthic and littoral invertebrates and fish were collected at four sites in the lower Mulgrave River under a range of flow conditions. Wet-season flooding caused significant reductions in instream productivity, whereas habitat disturbance reduced densities and abundances of littoral and benthic invertebrates. However, volumetric gut contents of 1360 fish, from 36 species, revealed seasonal shifts in guild membership by only two species, with fish moving between sites to target their preferred prey items – largely irrespective of differences in habitat structure. As a result, the food consumed by the fish community present at each site closely reflected the seasonal availability of food resources. The present paper questions whether fish community composition in small tropical rivers can be accurately predicted from habitat surrogates alone and encourages consideration of constraints imposed by the trophic dynamics and reproductive ecology of fish.