We present the results of studying the Holocene sediments of Bolshie Toroki Lake, a shallow brackish lake with carbonate sedimentation and high bioproductivity, located in the eastern part of Baraba lowland (southwestern Siberia). The mineral component of bottom sediments was studied by such methods as X-ray diffraction (XRD) analysis, IR spectroscopy, laser granulometry, elemental analysis, and others. By the mathematical modeling of complex XRD patterns, Mg-calcites with different Mg contents and aragonite have been established in the assemblage of carbonate minerals. Their structural and crystallochemical features and quantitative ratios were determined. The obtained high-resolution carbonate record was compared in the dated section with the distribution of the ash content, which is determined by the bioproductivity of the basin, and with a number of geochemical indicators of climate changes. The use of such a complex approach allowed us for the first time to recognize four stages in the evolution of Bolshie Toroki Lake; these stages were caused by cycles of drying/wetting of the regional climate and fluctuations of the lake level in the second half of the Holocene. Stage I (middle of the Atlantic) corresponded to the formation of the lake; stage II (second half of the Atlantic) was characterized by shallowing of the lake in a dry and warm climate; stage III (most of the Subboreal), shallow basin in a dry and cool climate; and stage IV (from the end of the Subboreal until the present) was marked by an increase in the water level of the lake and climate humidization.