Viss oxbow lake is located in Northeastern Hungary whose formation comes from the Bodrog river regulation. The oxbow lake was segmented to support angling and agricultural activities, plus a non-intervened section. This research aimed to identify the composition of the subfossil Cladocera assemblage, and to evaluate their composition along two environmental variables. The methodology included: Core sampling, Loss on Ignition, microscopic identification, and Non-Metric Multidimensional Scaling with Cord index. We found that 4 families (Bosminidae, Chydoridae, Daphniidae, and Leptodoridae) and 35 Cladoceran species were composing this subfossil Cladocera assemblage. We proved that the activities performed on each section were related to the change in the assemblage as to diversity and species dominance. We provided evidence on the role of macrophytes as biodiversity hotspots, on the importance of maintaining natural sections in these ecosystems, and on the high indicator value of Cladocerans. Finally we encourage to keep oxbow lakes under good ecological management due to their value as biodiversity reservoirs.