The Kambala and Barchin brackish lakes (Baraba steppe, southern West Siberia) contain an organic-rich sapropel layer that was formed in oxygen-depleted waters. We measured the bulk sediment elemental composition, the water chemistry and determined the mineralogical composition and predominant biota species (Diatoms and Cyanobacteria in phytoplankton community respectively) in the lakes. The result indicates that the first lake has a siliceous type of sapropel and the second a carbonaceous one. A computer thermodynamic model was developed for chemical interaction in water-bottom sediment systems of the Kambala and Barchin Lakes. The surface sodium bicarbonate waters are supersaturated with respect to calcite, magnesite (or low Mg-calcite), quartz and chlorite with minor strontianite, apatite and goethite (pH 8.9–9.3, Eh 0.3 V). Nevertheless, it is shown that during sapropel deposition, deep silt waters should be anoxic (Eh<0 V). The virtual component CH2O has been used to create an anoxic environment suitable for pyrite formation due to the biotic community impact and abiotic reduction. Thermodynamic calculation has shown that silt water is not necessarily euxinic (anoxic and sulfidic). Depending on Eh, sulfate sulfur can dominate in solution, causing the formation of gypsum together with pyrite. An attempt was made to find a reason for solution supersaturation with respect to Ca and Mg ions due to their complexation with humic acids.