Wet season freshwater flows deliver catchment nutrients (terrestrial and freshwater) to tropical estuaries that stimulate productivity and support consumers. However, the impact of flows on species in the adjacent nearshore is unclear. We investigated how freshwater flows affected the biochemical fingerprint, and by extension the resource use patterns, of the commercially important penaeid prawn, Penaeus merguiensis, in estuarine and nearshore habitats in the tropical Gulf of Carpentaria, Australia by comparing trace element and δ13C values of prawns across wet and dry seasons. We hypothesized wet season flow would increase resource homogenization, leading to similar biochemical profiles in prawns across these habitats. We identified an estuary-nearshore gradient in both trace element and δ13C values, with nearshore prawn profiles indicative of mixed catchment and marine contributions. Contrary to our hypothesis, there were seasonal changes in estuarine but not nearshore prawns, suggesting catchment resources were incorporated indirectly, rather than directly during high flow, into the nearshore food web, possibly via biogeochemical transformation processes. Therefore, nearshore prawns may be vulnerable to long-term flow disruptions.