Aquatic ecosystems are undergoing various changes due to natural and anthropogenic stressors. Paleolimnological approaches can be used to trace the environmental changes that have occurred in a water body and its catchment by examining the physical, chemical, and biological information, or proxies, preserved in sediment cores, and to determine the timing and extent of these changes. Our research aimed to study past environmental changes, reconstruct different aspects of the past ecosystem, and investigate the different utilization of Lake Vekeri by examining Cladocera remains preserved in the sediment. Our sampling site was Lake Vekeri, which is located in the Eastern Hungarian region. We collected a 10 cm long short sediment core with a gravity corer. The core was sliced every centimeter, and we examined the subfossil cladoceran remains from each sediment sample (slices). We identified the remains at the species level and we also estimated the content of the organic matter and CaCO₃ of the sediment samples. According to our results for the analysis of the subfossil Cladocera community, we are able the reconstruct past environmental changes and the effects of the different utilization methods on the ecosystem. The results offer crucial insights for comprehending the lake's ecosystem and to prove that the examination of the subfossil Cladocera community is an important tool for paleolimnological reconstruction.