Chemical composition of bottom sediments and pore waters of organic-mineral sediments (sapropel) of Lake Kotokel (Eastern Baikal region) has been studied, based on long drilling cores, 14.5 and 16.5 m. A reduction type of diagenesis has been established, during which destruction of organic matter, transformation of the chemical composition of pore waters and the formation of authigenic minerals occur. Even in the uppermost intervals of sapropel, organic matter is being profoundly transformed and differs significantly in composition from that of bioproducers (plankton). The major role in diagenetic transformations of organic matter belongs to different physiological groups of microorganisms, primarily heterotrophic, amonifying and sulfate-reducing bacteria. During diagenesis, the basic chemical composition of pore waters (HCO3–, SO42–, Cl–, Ca2+, Mg2+, K+, Na+) changes, trace elements (Fe, Mn, Sr, Ba, Pb, As, Co, Ni) redistribute, concentrations of HCO3–, NH4+, PO43− and Si increase; this is caused by destruction of organic matter. In the process of bacterial sulfate reduction in pore waters, the concentration of SO42– decreases along the depth of the section, and in the sediment the proportion of reduced forms of sulfur increases and the isotopic composition of sulphur δ34S changes. Transformation of chemical composition of pore waters and the activity of microorganisms leads to the formation of authigenic pyrite, rhodochrosite, and barite.