Floods are extreme weather events that can rapidly change water quality in receiving estuaries. The delivery of nutrients to the coastal zone via floods may stimulate productivity; however, in urban areas, the degradation of water quality and influx of contaminants can negatively affect inhabiting biota. Determining flood effects on inhabiting biota is important for informing catchment management practices. We investigated the body condition response of a commercially important prawn species, the brown tiger prawn Penaeus esculentus, to a large cyclone-driven flood in an urbanized subtropical coastal bay. Prawns were caught 10 days before the flood, 11 days after the flood, and 53 days after the flood in bare substrate areas of central Moreton Bay in Australia. Stable isotopes (δ15N and δ13C) were determined for prawn muscle tissue, and lipid content and a length-weight (Fulton’s K) index were used to assess prawn body condition. There were two distinct isotope signatures of tiger prawns living in either riverine or marine influenced areas, suggesting different residency areas within the bay. A flood signal (lower δ13C values post-flood) was detected in prawns in the southern area closest to the Logan River. Condition indices showed a short-term increase in condition of prawns in these southern sites, with no apparent condition change in prawns at other sites. A concurrent pulse in benthic primary productivity (chlorophyll a biomass) was measured in this southern area. Our results suggest that nutrients from the flood stimulated benthic primary production that was transferred through the food web, with positive impacts on prawn nutrition at southern sites. With an expected increase in unpredictable weather, including floods, under a changing climate, understanding short- and long-term ecosystem responses in modified catchments is important for mitigating sediment erosion and estuarine and coastal infilling effects, while maintaining productivity benefits to fisheries in receiving estuaries.