The Tazheran lakes are located compactly in the small Tazheran steppe area. Their bottom sediments are predominantly various calcite–dolomite carbonates, and their waters are rich in uranium. The studies have shown that the main process in these lakes is chemogenic carbonate precipitation with the participation of carbon dioxide formed through the bacterial destruction of organic matter. For thermodynamic modeling of the composition of bottom sediments, we chose two lakes with different basic parameters. Calculations were made for the 15-component heterogeneous system H2O–Na–Ca–Mg–K–Sr–Ba–Si–Al–Cl–C–S–Fe–U–Mn including particles in the solution, minerals, and gases at 25 °C and 1 bar. As starting information, we used the obtained analytical data on the natural composition of waters and bottom sediments. The results show that calcite–dolomite carbonates are predominant in the bottom sediments and the destruction of organic matter results in reducing conditions. This confirms the hypothesis of the formation of mineral phases of U(IV) during diagenetic processes in the bottom sediments of the studied lakes.