Paleoenvironmental and paleoclimate changes in intracontinental Siberia were reconstructed by continuous, high-resolution records (biogenic silica, U, total organic carbon and N, total S, and grain size) from a sediment core retrieved from the Buguldeika Saddle, Lake Baikal, dating back to the last 33 cal. ka BP. The Holocene climate was wet relative to the last glacial period. The climate became gradually warm and wet from the early to middle Holocene, followed by a shift at ca. 6.5 cal. ka BP toward warm and dry, possibly because of evapotranspiration. This suggests that the climate system transition from the glacial to interglacial state occurred at that time. In the last glacial, the deposition of carbonate mud from the Primorsky Range was associated with Heinrich events (H3 and H1) and the Selenga River inflow during the Last Glacial Maximum was caused by meltwater of mountain glaciers in the Khamar–Daban Range. The anoxic bottom-water during the Allerød-Younger Dryas was probably a result of weakened ventilation associated with reduced Selenga River inflow and microbial decomposition of organic matters originating from moderate input of nutrients from the Primorsky Range. The rapid decline in precipitation during the early Holocene may have been a response to the 8.2 ka cooling event.