The ecological effect of prawn trawling on the benthos of the Gulf of Carpentaria, northern Australia, was investigated by examining stomach contents of common demersal fishes incidentally caught as by-catch in the fishery. Fishes were collected from high and low fishing intensity sites in three regions based on vessel monitoring system data. The diets of eight species of benthic fish predators were compared between regions and fishing intensities. A regional effect on diet was evident for seven species. Only one generalist species had no significant difference in diet among the three regions. For the comparisons within each region, five predator species had significantly different diet between high and low fishing intensities in at least one region. Across the three regions, high fishing intensity sites had predators that consumed a greater biomass of crustaceans, molluscs and echinoderms. At low fishing intensity sites, predators had diets comprising a greater biomass of cnidarians and teleosts, and a different assemblage of molluscs, crustaceans and fishes. These changes in diet suggest that there may have been a shift in the structure of the benthic community following intensive fishing. Analysis of predator diets is a useful tool to help identify changes in the benthic community composition after exposure to fishing. This study also provided valuable diet information on a range of abundant generalist benthic predators to improve the ecosystem modelling tools needed to support ecosystem-based fisheries management.