The authors own and literary data on long-term paleogeographical research of Lake Onego and its drainage basin carried out using a set of methods are summarized in the article. The deglaciation, transgressive-regressive activity of Lake Onego, time and features of the formation of small lakes, their water level regime and the transition of some of them to a telmatic development pathway are discussed. According to available data, deglaciation of the study area began at ~ 13000–14000 BP. The deglaciation of the lake was completed at 11600 BP and that of the modern catchment at the end of the Alleröd. The water level of the newly formed periglacial Lake Onego was variable. As the level was decreasing starting from around 12300 BP, small and medium-sized paleolakes became separated and isolated in depressions. There also formed lakes produced by stagnant ice melting (from the Alleröd to the end of the Boreal Period) and lakes in areas not flooded by periglacial waters. The formation of organic sediments in the lakes is shown to have commenced at ~ 10300 BP. Peat accumulation in shallow depressions also began in Preboreal time and that in the near-shore zone of the investigated paleolakes in Boreal time. Most of them were filled with peat by the end of the Sub-Boreal period. Vegetation dynamics was reconstructed from the Middle Dryas (DR2, ~12000 BP) to the present as related to changes in the environment, including the paleoclimate and hydrology of the territory, and taking into account the geomorphology of the territory and human impact. It was established that the composition and dynamics of vegetation in the Late Glacial and Holocene were controlled by climatic factors, while their distinctive characteristics by geologo-geomorphological factors. Plants were dispersing as the territory was liberated from ice and periglacial waters. The latter, as well as residual arrays of stagnant ice, delayed the formation of the plant cover.