—A quantitative assessment of the fractionation of elements during sedimentation is made based on long-term comprehensive studies with the participation of geochemists, hydrobiologists, soil scientists, and chemists. Analytical studies of the chemical composition of water, soil, bottom sediments, and biota were carried out at the Center for Collective Use of Scientific Equipment for Multielement and Isotope Studies and at the Institute of Catalysis, Novosibirsk. Based on a mineralogical and geochemical approach, we chose lakes with different types of biogenetic formation and different classes of organomineral sediments and performed detailed studies of the relationship between the organic and mineral parts of the sediments. It has been established that the organomineral sediments of different classes and biogenetic types of formation differ not only in the contents of major elements (Si, Ca, C, and O) but also in the group composition of organic matter. The direct effect of the transformation of organic matter on the mineral composition of bottom sediments has been revealed. The contents of other elements vary in a narrow range of values. At the same time, the difference in the contents of elements between organomineral sediments of different types and classes is comparable with their difference within a class. The leading role in the formation of the geochemical and mineral compositions of the organomineral sediments of small lakes belongs to intricate biological, biochemical, and physicochemical processes depending mainly on azonal factors and occurring under prolonged freezing-up (anaerobic conditions).