We assessed the usefulness of Cladocera remains for establishing the ecological status of oxbows and also tested the association of Cladocera species with various vegetation types. Cladocera remains were collected from the surface sediment of four habitat types (tangled vegetation, open water, reeds and tunnels) and 15 physical and chemical parameters of surface water were studied. In the surface sediment samples, we identified 32 Cladocera taxa. There was a significant difference in the number of species amongst habitat types as per ANOVA. The benthic and plant associated Cladocera communities of reeds, tangled vegetation, open water and tunnels were clearly separated from each other by NMDS ordination. CCA showed that habitat types had characteristic Cladocera species: Pleuroxus species were frequent in the tangled vegetation habitat, while Chydorus species were frequent in the open water. Remarkably, in reeds, Bosmina species were frequent, although these species are usually common in open water. Specimens of the Alona genus were found everywhere. Our findings suggest that the remains of Cladocera species may be useful indicators to assess and monitor the structure of freshwater lakes.