—We present results of research into the mineral composition of the Holocene sediments of Lake Malye Chany of the Chany lake system located in the Baraba steppe and comprising three lakes: Bol’shie Chany, Malye Chany, and Yarkul’, connected by channels. The sediments were studied by XRD, IR and Raman spectroscopy, laser granulometry, analysis of stable 18O and 13C isotopes, elemental analysis (XRF), etc. Mineral analysis has revealed predominant quartz, feldspars, and carbonates and subordinate gypsum, bassanite, pyrite, mica, chlorite, and kaolinite. Mathematical modeling of the XRD spectra of carbonates, using Pearson VII function, made it possible to identify the carbonate phases and determine their quantitative proportions. The obtained high-resolution carbonate record providing information about the stratigraphic distribution of carbonates in the dated section was compared with the available lithological, geochemical, and isotope data. Based on these data, we have reconstructed five stages of the Holocene evolution of the Malye Chany basin. It is shown that the proportions of minerals in the section vary in accordance with the lake level fluctuations in the alternating periods of the Holocene regional arid and humid climate. We compared the mineral compositions of the bottom sediments of Lake Malye Chany and Yarkovsky Pool of Lake Bol’shie Chany. The revealed mineral assemblages reflect the local specifics of the lake system and the influence of natural and climatic factors on the inland sedimentation processes.