East European lake-river systems have hydrological regimes typical for continental climate zones. The Postglacial development of the basins and regional palaeoclimatic pattern in the Holocene implied a specific succession of biota communities passing through lakes’ subsequent stages in the water level, trophic state and habitat availability. The Great Serteya Palaeolake Basin is the largest palaeolake within the Serteyka lake-river system, which has been functioning since the Late Weichselian (Vistulian). Presented below is a multi-proxy study on the sequence from the paleolake within the present-day valley. During the Late Weichselian, it formed an astatic, and later a permanent, water body of Postglacial origin. The associated melting, flooding and aeolian processes acted as sources of various Late Weichselian sediments. Summer mean air temperature drove the lake ecosystem development. The Holocene Thermal Optimum in 8.5–7.7 kyr cal BP was followed by subsequent lower temperature. There is weak evidence of coole oscillations at 8.2 kyr cal BP, 7.0–6.8 kyr cal BP and 5.8–5.9 kyr cal BP and the Little Ice Age (480–395 yr cal BP), until modern time (−65 yr cal BP). Five stages of lake ecosystem development were identified based on the biota: 1) an initial stage during the Late Weichselian with glaciolacustrine and later lacustrine accumulation of inorganic deposits, 2) the stage with Cladocera as a leading indicators of mesotrophic water body with a well-developed pelagic zone supplied by early spring floods of the Serteyka River, carrying melting snow and ice floes to the lake basin, 3) the stage dominated by Chironomidae and diatoms typical to high trophic states reflecting widespread open bottom sediment and macrophyte habitats 4) a stage with distinct Neolithic community impact reflected by macrofossils remain after pile-dwelling settlement, fish and aquatic plants consumption 5) a final stage dominated by diatoms typical to shallow, semi-permanent, eutrophic bulrush swamp.