Stable isotopes (δ13C and δ15N) and gut contents were analysed for two species of co-occurring native and exotic fish in three shallow water bodies within an Australian riparian wetland system. During a period of hydrologic recession we found depletions in δ13C of up to -25‰for algae and -2‰ for sediment organic matter (SOM). The native Hypseleotris sp. (carp gudgeon) and the exotic Cyprinus carpio (common carp) were depleted in δ13Cup to -3.2‰, indicating that the SOM was the dominant dietary source of carbon for the two species of fish in both high- and the receded low-water conditions. In the low-water conditions, however, there was a five-fold increase in the occurrence of insects in the gut of the exotic C. carpio and the trophic positions of C. carpio and Hypseleotris sp. were more similar in all three water bodies than at high-water conditions. Our results indicate that there were shifts in dietary sources and trophic positions during hydrologic recession and provide evidence that flow reductions in wetland systems can increase the dietary overlap between native and exotic fishes.