We studied recent sedimentation in small saline and brackish lakes located in the Ol’khon region (western Baikal area) with arid and semiarid climate. The lakes belong to the Tazheran system; it is a series of compactly located closed shallow lakes, with a limited catchment area and different mineralization, under the same landscape, climatic, geologic, and geochemical conditions. Two complementary approaches are applied in the research: (1) a detailed study of individual lake and (2) a comparison of the entire series of lakes, which can be considered a natural model for studying the relationship between endogenic mineral formation and the geochemistry of lake waters. The lake waters and bottom sediments were studied by a set of modern methods of geochemistry, mineralogy, and crystal chemistry. The mineral component of the bottom sediments was analyzed by powder X-ray diffraction (XRD), IR spectroscopy, and electron microscopy. The lakes are characterized by predominant carbonate sedimentation; authigenic pyrite, smectite, chlorite, and illite are detected in assemblage with carbonate minerals in the bottom sediments. Carbonate phases have been identified, and their proportions have been determined in the samples by decomposition of the complex XRD profiles of carbonate minerals into peaks using the Pearson VII function. Mathematical modeling of the XRD profiles of carbonates has revealed that predominantly Mg-calcites with variable Mg content and excess-Ca dolomite accumulate in lake bottom sediments influenced by biogenic processes. Aragonite, monohydrocalcite, and rhodochrosite form in some lakes along with carbonates of the calcite–dolomite series. We show a dependence of the composition of the assemblages of the newly formed endogenic carbonate minerals and their crystallochemical characteristics on the chemical composition of lake waters.