In a restored wetland (South of Spain), where different flow regimes control water exchange with the adjacent Guadalquivir estuary, the native Palaemon varians coexists with an exotic counterpart species Palaemon macrodactylus. This controlled m\acrocosm offers an excellent opportunity to investigate how the effects of water management, through different flow regimes, and the presence of a non-native species affect the aquatic community and the trophic niche (by gut contents and C-N isotopic composition) of the native shrimp Palaemon varians. We found that increased water exchange rate (5% day(-1) in mixed ponds vs. 0.1% day(-1) in extensive ponds) modified the aquatic community of this wetland; while extensive ponds are dominated by isopods and amphipods with low presence of P. macrodactylus, mixed ponds presented high biomass of mysids, corixids, copepods and both shrimp species. An estuarine origin of nutrients and primary production might explain seasonal and spatial differences found among ponds of this wetland. A combined analysis of gut contents and isotopic composition of the native and the exotic species showed that: (1) native P. varians is mainly omnivorous (2) while the non-native P. macrodactylus is more zooplanktivorous and (3) a dietary overlap occurred when both species coexist at mixed ponds where a higher water exchange and high abundance of mysids and copepods diversifies the native species' diet. Thus differences in the trophic ecology of both species are clearly explained by water management. This experimental study is a valuable tool for integrated management between river basin and wetlands since it allows quantification of wetland community changes in response to the flow regime.