A key ecological function of benthic communities is provision of prey for higher trophic level predators such as fish and birds. Assessments of benthic communities and their drivers is typically based on counts of individual organisms. This potentially provides a limited picture, particularly when trophic functioning is of interest. We measured individual counts, biomass, and energy density of benthic macroinvertebrates throughout the estuary of Australia’s largest river system from 2019–2023, a period encompassing the largest flood event in the Murray River since 1956. Biomass and energy revealed different patterns in prey assemblage structure compared to individual counts. There were minor differences in assemblage structures based on biomass and energy. Energy content was used to construct prey quality profiles – a novel technique for characterising prey quality across an assemblage of different taxa or functional groups. These profiles revealed that the flood caused overall decreases in abundance of prey but also increases in the proportion of high-quality prey, which may have helped to buffer the impact on predators, and may have improved foraging conditions in some areas. Quantifying biomass or energy density of the constituent species in a community can provide different insights into prey landscape dynamics than count-based assessments.