The article presents the studies on understanding the chemical evolution of Maloye Yarovoe lake that is located in the semi-arid landscape of and represent the most widespread chemical type of saline lake (Cl-Na) on the territory of Kulunda steppe (south of Western Siberia). The lake has gone through several changes in its state which are well represented in its sediments: section 1 (4.52–4.97 m) represents the subbase; section 2 (3.0–4.57 m) corresponds to a “shallow lake” stage and contains two sublayers; section 3 (0–2.25 m) illustrates an increase in erosion of the shoreline and corresponds to a “deep lake” stage. The extrapolation of radiocarbon dates suggests that the most significant changes in the state of the lake occurred at about 6.5–7.1 ka BP (transition from a small lake to a large one with intensified coastal erosion) and at about 5.69 and 3.5 ka BP (increase in the organic component). The results of sequential extraction of elements correspond to chemical changes occurred in a certain time of the lake state by changing in their distribution level and fraction type along the core. The results of lake water evaporation and organic matter degradation modelling performed in Phreeqc for oxic and anoxic condition showed the following stages of chemical divides could be expected in case of further lakes desiccation: Halite— Epsomite—Bischofite/Carnalite with possibility of Nahcolite precipitation in carbonate enriched periods (summer and autumn periods of organic matter degradation). Water–rock interaction processes in combination with biogeochemical reactions affect drastically not only the migration features of elements in water and sediments, but also the type of mineral crystallization in lake sediments.