This study presents the first centennial‐scale multi‐proxy record from the East Sayan Mountains, which are part of the central Asian ‘water tower’ massif. The record from Lake Kaskadnoe in the Jom‐Bolok area shows changes in vegetation and climate since c. 14.2 cal. ka BP. Although the study site is in an area with active volcanism, there is no clear evidence that volcanic eruptions influenced the local vegetation. At c. 14.2–12.9 cal. ka BP, regional climate was sufficiently warm and moist to allow scattered growth of Picea, Larix and Betula nana around the lake. A cooling episode at c. 12.9–11.5 cal. ka BP is coincident with the Younger Dryas and led to the predominance of shrub tundra in the basin. Cool and moist conditions c. 11.5–9.0 cal. ka BP resulted in the spread of Pinus sibirica in the catchment of Lake Kaskadnoe. The Middle Holocene, c. 9.0–4.5 cal. ka BP, featured a warmer and drier regional climate, which led to a decrease in high‐elevation dark conifer forest. Subsequently, the onset of the Neoglacial and a cooler climate is indicated by the spread of Larix sibirica and Pinus sibirica in the study area. Lateglacial and Holocene moisture conditions in the East Sayan Mountains have primarily been controlled by the interaction of the westerlies and the East Asian Summer Monsoon and show a drying trend through time; long‐term insolation changes affected both the Monsoon and regional temperatures. The pattern of moisture decrease in the latter part of the Holocene is seen at sites in adjacent regions of the central Asian mountains.