Sapropels, biogenic lake sediments, are characterized by a reduction type of diagenesis, during which decomposition of organic compounds, modification of the pore water chemical composition and precipitation of authigenic minerals, mostly pyrite, occur. Pyrolysis data indicate that organic matter undergoes radical transformations already in the uppermost sapropel layers, and composition of the organic matter in the sediments is principally different from the composition of the organic matter of live organisms, which produce the sediments. The sapropels lose labile protein–carbohydrate compounds in the horizon of unconsolidated sediment (0–5 cm), and kerogen appears, whose macromolecular structures start to develop in the very early stages of diagenesis. Various physiological groups of microorganisms provide diagenetic transformations of the organic matter, where heterotrophic, ammonifying and sulfate-reducing bacteria play key role. Their effect is well-seen from the pore water transformation: a decrease in concentrations of SO 4 2− and consequent increase of reduced Fe and S as pyrite in the solid phase of the sediment. Comparative analysis shows that, unlike in lakes of the Baikal area, sapropels in southern West Siberia are affected by more active sulfate reduction, which can depend on both the composition of the organic matter and the SO 4 2− concentration in the pore waters.