The chemical and microbiological composition of sapropel was investigated in the 7 m Holocene sediment core of Lake Dukhovoe. Sapropel is mainly formed from phytoplankton. Heterotrophic bacteria play the main role in the decomposition of organic matter in this sapropel, with the formation of organic-mineral complexes. A reducing type of diagenesis was established in the sapropel. Processes of sapropel transformation under the influence of mechanical, biochemical, microbiological, and physicochemical processes lead to the formation of geochemical barriers and new phases (organic-mineral complexes, diatomite, pyrite inside the cyst of Сhrysophyceae, framboidal pyrite, vivianite, carbonates, etc.), as well as the accumulation and leaching of elements.