—The bottom sediments of lakes with different mineralization located in the basins of inland areas are high-resolution archives of climate and environmental changes. We present results of study of the Late Pleistocene–Holocene sediments of freshwater Lake Baunt, one of the lakes of the Baunt (Tsipa) depression in the permafrost zone in northern Buryatia. The sediments were studied by XRD, IR spectroscopy, laser granulometry, elemental analysis, AMS dating, etc. Mineral analysis of the bottom sediments with an age of ~18 ka has revealed predominant phyllosilicates, quartz, and feldspars. Mathematical modeling of complex XRD spectra made it possible to identify chlorite, muscovite, illite, mixed-layer illite–smectite and chlorite–smectite, and kaolinite among the phyllosilicates. We have determined their structural and crystal-chemical features and quantitative proportions in the section (800 cm long core), which vary in accordance with the climate cycles and lake level fluctuations. The results obtained helped to reconstruct the evolution of the Lake Baunt basin controlled by the regional climate throughout the Late Pleistocene–Holocene. This paper continues a series of our publications concerned with the reconstruction of the Late Pleistocene–Holocene climate in East Siberia by comprehensive studies of the mineral composition of sedimentary sections of small lakes.