—Bottom sediments of lakes are regarded as one of the most informative continental facies used to reconstruct environmental changes in lake catchments. They usually contain a high-resolution and continuous record of geologic events, the knowledge of which is important for understanding the evolution of sedimentary processes and landscapes under the influence of climatic changes and the impact of short-lived catastrophic processes. The southwestern Baikal region (the Tunka rift and its East Sayan mountain framing) is replete with lakes of different geneses and morphologies. Recent fieldworks have allowed a multiproxy study of the lacustrine sediments of several lakes of the Oka and Tunka regions. The results demonstrate that there were no glaciers in the foothill plain of the Tunka rift valley earlier than 14,800 cal yr BP. On the Oka plateau, within the East Sayan high-mountain zone, deglaciation started somewhat earlier than 13,800 cal yr BP. The grain size, petromagnetic, and physical properties of the lacustrine sediments point to a general weak hydrodynamics throughout the 13,800 yr sedimentation history in Lake Khikushka. However, a gradual reduction in fine fractions from base to top of the lake section suggests a gradual drawdown of the water level following the change of the water source from glacial melt waters to atmospheric precipitation. Biogenic silt accumulation in Lake Khikushka started parallel with the onset of the Holocene ~11,700 yr BP, suggesting a quick response of the natural environment of the lake basin to major global climatic changes. The short-term episodes of enhanced hydrodynamics in Lake Khikushka ~9000, 8200, 6500, and 2000 yr BP confirm the high sensitivity of the lake geosystem to climatic changes, not only on a millennial but also on a shorter-time scale. The characteristics of the sediments of Lake Engarginskoe are evident of lacustrine-alluvial sedimentation in the reservoir in the Early and Middle Holocene. New data on the grain size and petromagnetic parameters of the lacustrine sediments from two lakes located within different climatic belts of East Sayan show their high potential for a wide range of paleoecological reconstructions.