While flow regime is widely recognised as an over-arching feature structuring aquatic ecosystems, the influence of flood events on feeding habits in fish assemblages inhabiting variable environments remains largely unknown. In this study, we investigated how diets of a fish assemblage changed in response to fluctuations in hydrology in a highly variable, wet-dry tropical Australian river. We compared dietary habits, trophic guilds and intra- and interspecific dietary overlap and diet breadth across different seasons. Wet-season floods acted as major geomorphic and ecological perturbations that exerted substantial effects on the trophic dynamics of the terapontid assemblage, particularly through the removal of in-stream plant production and detritus. Forced by major shifts in food source availability due to seasonal flooding, fishes responded to these perturbations by marked changes in diet, with significant guild switching following wet-season floods. Rather than the predictable, gradual, changes in consumer–resource interactions associated with the gentler seasonal flood pulse evident in other tropical river systems, study results instead emphasised rapid and profound changes to species' diets and trophic interactions following abrupt flood pulses. These sudden shifts in food sources may also explain some of the lack of clarity in discrimination of specific carbon sources or species' trophic levels evident in isotopic food web studies from the region. Results indicate that the effects of flood pulses on assemblage trophic interactions may differ among ecosystem types and across the broad potential scale of hydrological disturbance mediated by flood events.