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Eutrophication of shallow lakes often triggers a series of cascading ecological effects. Among these are shifts in the zooplankton community structure due to phytoplankton changes, or shifts in the fish community reducing size-selective feeding of planktivorous fish. In such conditions, larger zooplankton (e.g. Daphnia) can have a selective advantage. Re-oligotrophication can reverse such food-web interactions. Europe’s largest wetland system (the Danube Delta) went through a period of eutrophication and is now slowly recovering again. However, changes in the Daphnia populations triggered by eutrophication in this system have remained unstudied. We used different sampling strategies to screen 24 lakes (which differ in their ecological state) for the presence of Daphnia as well as for biotic and abiotic parameters potentially explaining Daphnia abundance. Daphnia densities were surprisingly low. We found D. magna ephippia in the sediment, but no D. magna in the water column. Microsatellite analyses on pelagic Daphnia populations confirmed the presence of the D. longispina complex and provided evidence for significant hybridisation events. FluoroProbe data showed that Daphnia was mainly present in lakes with a higher phytoplankton production. Our study provides insights into the spatial and temporal distribution of Daphnia in a very dynamic wetland system.