Lake Velencei is the third biggest lake in Hungary, and it is divided into three parts: protected, transitional, and recreational areas. We collected sediment, surface sediment, and water samples from these areas and then we examined the subfossil Cladocera remains. Our objective was to assess the ecological fragmentation of Lake Velencei by examining the occurrence and distribution of the cladoceran taxa in relation to various environmental conditions, including sediment and water chemistry. For sediment sampling, 10 cm long cores were collected from the three different utilisations, with two cores from each area using gravity corer. For subfossil Cladocera analysis, we used 2 cm slices from each core, and 1 cm³ sediment was explored. In this study, we identified subfossil Cladocera remains at the species level, providing a detailed understanding of the biodiversity and community structure within each area. Our research showed that the Cladoceran species composition and the number of individuals reflect the utilization of the separated areas. Also, the study demonstrated that the transitional area is separated between the nature reserved area and the recreation area based on sediment chemistry. The distribution of cladocerans in the surface sediment, and their relation to these important environmental variables, suggests that there is considerable potential for the use of sedimentary cladoceran remains as environmental indicators similar to the water and sediment chemistry parameters.