A major parallel between soils and lake sediments is found in the role of microorganisms decomposing the organic substances. However, the two systems are not fully comparable: the typical horizons of land soil are lacking in sediments under water. Oligotrophic lake sediments differ in various aspects from the sediments in eutrophic lakes. Depending on the amount and type of organic substances provided, different processes of microbiological activity create major changes in redox potential, acidity, and biochemical changes, Mineralization, nitrification, denitrification, methane production, and sulfate reduction contribute to the geochemical situation of the lake sediment. The carbonate cycle, the formation of iron-manganese deposits, and the silica cycle in lakes are discussed in more detail. The calcium carbonate equilibrium is found to be largely controlled by microbial effects on carbon dioxide concentration. Formation of iron-manganese concretions takes place at the contact-surface between the reducing zone of the sediment and an upper oxidizing layer. Oxidation of the more soluble iron and manganese compounds into less soluble oxides takes place through the agency of various microbes. These microbes are found with the aid of a capillary technique only. The silica transported after weathering into the lakes was found to be in a complex association with organic substances; subsequent decomposition of these complexes by microorganisms leads to the precipitation of silica in the form of its polymers (opal, quartz).