The 3 ka chronology of climatically driven glacier fluctuations and upper tree limit variations, dates of strong prehistoric earthquakes, and fluvial system transformation are established for the SE Altai (mountains of South Siberia) on the basis of radiocarbon and dendrochronological dating. This time period of prosperity of the Altai nomadic cultures is characterized by more arid and cold climate in comparison with the first half of the Holocene. During the last 3 ka, glacier advances occurred at 2300–1700 cal. BP (Historical stage) and 13th–19th centuries (Aktru stage (LIA)). The recurrence interval of strong prehistoric earthquakes is estimated as ∼400 years. The final draining of the Holocene lake in the Chuya intermountain depression took place about 1500 cal. BP. All these natural events together with political and social factors controlled the nomadic population, their habitat, and the patterns of evolution and migration of nomadic cultures within the SE Altai. Aridity intensification and cooling enhanced by anthropogenic impact brought deforestation of the eastern part of the Chuya depression.