We studied 46 small, drainless lakes in various landscape types: The sub-taiga (Vasyugan plain), forest–steppe (Baraba lowland), and steppe and subzone of ribbon forests (Kulunda plain). Sampling of lake components (sediments, water, and biota) was performed. The materials were analyzed via a combination of modern analytical methods (atomic absorption spectroscopy, X-ray fluorescence, scanning electron microscopy and X-ray diffractometry). It was found that in the south of Western Siberia, lakes with a bicarbonate-sodium water composition are widespread against the background of general landscape zoning. This composition contributes to the abundant growth of biota in the lakes, which leads to the processes of authigenic carbonate formation from calcite–dolomite series and aragonite on geochemical barriers, i.e., drifting biota–water, submerged biota–water, and water–bottom sediments against a background of terrigenous demolition and organic matter accumulation. The article shows the differences in the composition and structure of low-temperature carbonate minerals formed on various geochemical barriers. It was found that low-magnesium calcite and aragonite are the most common authigenic carbonates in small lakes in the south of Western Siberia and are formed on all three geochemical barriers in lakes. High-magnesium calcites and Ca-excess dolomites are formed only at the water–bottom sediment barrier in lakes with HCO3
–Na and Cl–HCO3
–Na water composition at pH > 9 and with a total dissolved solids > 3 g·L−1
(in some lakes of HCO3
-Na composition with a TDS < 3 g·L−1
and pH > 9).
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