Zooplankton in estuaries encounter complex physical and biogeochemical processes that affect the quantity, quality and origin of their food sources. The knowledge about how zooplankton deal with highly variable organic matter sources is sparse. Here, we investigated the spatial and temporal patterns of zooplankton trophic dynamics and carbon sources in the intensively dredged, eutrophic Elbe estuary. For this purpose, we applied elemental and stable isotope analysis (δ13C and δ15N) on particulate organic matter (POM) and dominant meso- and macrozooplankton species including ichthyoplankton from five stations along the entire salinity gradient of the estuary in 2022. The δ13C values of POM (-29.2 to -23.0 ‰) indicated a mixture of riverine, terrestrial and coastal carbon sources used by most taxa for their diet. Eurytemora affinis (-34.0 to -23.3 ‰) and Mesopodopsis slabberi (-22.2 to -20.0 ‰) exhibited a broader range in δ13C than POM, suggesting selective feeding on single POM components depending on the season. In winter and autumn, under high suspended matter loads and limited availability of high-quality autochthonous phytoplankton, zooplankton showed increased tendency for carnivory (higher δ15N values). Our study revealed a high trophic plasticity of estuarine Elbe zooplankton to buffer hydrological related alterations in their food source by dietary niche partitioning and a flexible switch in their feeding behaviour.