Our study aimed to conduct a paleolimnological reconstruction of a shallow lake, Lake Balaton, based on Cladocera remains. An up-to-date understanding of Cladocera remains is a crucial aspect of paleolimnological research. The lake's sediment provides large quantities of high-quality Cladocera species. Acquiring information onexploration is essential in order to reconstruct the palaeo history of the lake. The varying evolution of Keszthely Bay gave us a good opportunity to study the sediments' composition; this European lake is superficial and nutrient-rich. Sediment columns were taken in both Keszthely and Siófok Bays. One was used for geochemical analysis and the other was used for cladocera remains. The zooplankton and benthic Chydorid Cladocerans provided previously unavailable information on the historical development of planktivorous fish populations and lake production which is used to document introductions of exotic species and human disturbance around lakes. In January 2006 in Keszthely and in May 2006 in Siófok Bay, we collected one-meter-long columns of sediment (0.05 meters in diameter). Lake Balaton has chydorid-rich sediment, with species belonging to the Alona genus. The open water is rich in Daphnia cucullata and Daphnia galeata, but in the sediment layers, only a few Daphnia ephippia were found, and no Daphnia remains. Bosmina coregoni is numerous in recent plankton, but the remains of this species are on the uppermost sediment layers, indicating the changes in the trophic status of the basins. Thirteen cladocera species were found in the remains of the sediment of Siófok Bay. Chydorid remains were common along the core. Twenty-five cladocera species were identified by their remains in the sediment of Keszthely Bay. Meanwhile, the remains of planktonic cladocera (like daphnids and cosmids) are under-represented. The cladocera remains, the organic material content, the CaCO3 content, the mineral material content, and the sediment chronology were studied.