This paper presents results of biogeochemical investigation of the Holocene organic-rich sapropelic sediments of Lake Dukhovoe situated not far from the Baikal. The main source of organic matter in Lake Dukhovoe is phytoplankton, which serves as a biogeochemical barrier where elements are accumulated from water and then buried in the bottom sediments. Microorganisms (e.g., bacteria, micromycete and actinomycetes) play significant role in decomposition of organic matter and formation of organic-mineral complexes in four distinguished types of sapropels: organic, organic-mineral, mineral-organic and mineral. Diagenetic transformations of the Lake Dukhovoe sapropels under influence of mechanical, biochemical, microbiological and physicochemical processes lead to transformation of element speciation. A boundary between oxidizing and reducing diagenesis conditions is at the depth of 167 cm in the sapropel core. Change of the conditions forms geochemical barrier in bottom sediments and control the formation of secondary phases (organic-mineral complexes, diatomite, framboidal pyrite, vivianite, carbonates, etc.) as well as processes of accumulation and leaching of chemical elements. Additionally, high contents of Fe, Mn, Cu, Zn, Pb, Cd, and Mo in the upper 10 cm of the sapropel might have been caused by forest fires and anthropogenic factors. The fact of marcasite formation in the stomatocysts of Chrysophyte algae (golden algae) is new and was established for the first time. Based on the results and geochemical equilibrium modelling, the stomatocysts of Chrysophyte algae can be considered as a microreactor for iron sulfide formation.