Sediments of lakes located in closed basins in inland areas are an excellent archive of environmental and climatic changes. One of such archives is the Chany lake system located in the Baraba steppe of southern West Siberia and comprising three associated lakes: Bol'shie Chany, Malye Chany, and Yarkul’, connected by watercourses. We present the first data on the mineral composition of the Holocene sediments of Yarkovsky Pool of Lake Bol'shie Chany with predominantly carbonate sedimentation. The sediments were studied by X-ray diffraction (XRD), IR spectroscopy, scanning electron microscopy, 18O and 13C stable-isotope geochemistry, laser granulometry, elemental analysis, and radioisotope dating. Mathematical modeling of complex XRD profiles of carbonate minerals in the sediments has revealed Mg-calcites with different Mg contents, excess-Ca dolomites, and aragonite. The obtained carbonate record gives an insight into the stratigraphic distribution of chemogenic carbonates, in which the number and proportion of phases are determined by the Mg/Ca ratio, salinity, and total alkalinity of the lake water. The phase proportions change depending on climatic cycles and lake level fluctuations. Comparison of the carbonate record with the lithologic data, δ18O and δ13C values, and distribution of some geochemical indicators of sedimentary environments showed several stages of evolution of Yarkovsky Pool related to Holocene regional climatic changes.