The region of NW Russia connecting with the Baltic Sea presents a dynamic ecological system that was sensitive to environmental changes during the Holocene. Certain factors affected environmental changes in the region during the Holocene: deglaciation processes, that finally terminated about 9 cal ka BP; eustatic sea-level changes; and tectonic movements, which are basically considered in the region as isostatic uplift processes. Contextual remains of ancient human occupation sites can be the only evidence of surface stabilization in monotonous sediments, such as aquatic and subaquatic deposits. Prehistoric settlements also mark ancient shorelines. The latter is of great importance for studying the history of water oscillations and coastal-line displacements on the territory of NW Russia. The transgressive–regressive stages of the Baltic Sea (at c. 10.15 cal ka BP, the Ancylus transgression; at c. 7.6–7.0 cal ka BP, the Littorina transgression) have an impact on the positions of prehistorical sites. The complex investigations of the Stone Age archaeological settlements on the Karelian Isthmus and in the Dvina–Lovat’ basin, and their altitudes below sea level, allowed us to reconstruct palaeoenvironmental changes during the Holocene, the chronology of cultural–historical processes and the adaptation strategy of ancient people to environmental conditions in this territory.