The climate changes and related crucial environmental changes in the Late Glacial and Holocene in the Southern Baltic area can be investigated by mollusc and ostracod analyses. It is well known that accumulation of mineral and biogenic sediments in the Southern Baltic area began in the Late Glacial. The process took place in cold tundra lakes and mires. The presence of lake basins is confirmed by seismoacoustic investigations and the resulting 3D spatial model. Lacustrine sediments contain an assemblage of molluscs and ostracod fauna represented by freshwater species indicating cold climate, such as: Armiger crista f. cristatus, Gyraulus laevis, Lymnaea peregra, Pisidium casertanum, Pisidium casertanum f. ponderosa, Pisidium milium, Pisidium nitidum, Pisidium obtusale f. lapponicum, Valvata cristata, Pisidium conventus, Candona candida, Candona neglecta, Cytherissa lacustris, Darwinula stevensoni and Cypridopsis vidua. The accumulation in freshwater reservoirs was continued during the Early Holocene. Besides cold freshwater species, sediments of that age also contain freshwater species of molluscs and ostracods that required higher temperature: Bithynia tentaculata, Physa fontinalis, Pisidium amnicum, Candona compressa and Metacypris cordata. It indicates a climate warming in the Preboreal period. These lake sediments were partly destroyed and covered by marine sands during the Middle and Upper Holocene. Good indicators of changing from a freshwater to marine environment are the following marine species found in the sediments: Hydrobia ulvae, Hydrobia ventrosa, Cerastoderma glaucum, Mytilus edulis, Macoma balthica, Cyprideis torosa and Cytheromorpha fuscata.