This article considers the formation conditions of nonmetallic and ore minerals in limnogenic structures. Lakes naturally enrich a wide range of useful components – silicate, carbonate, water-soluble substances, ores, and organominerals. The most significant resources of modern lakes, apart from water, include sapropels, diatomites, lime, and mineral salts. Deposits of sand, clay, oil shale, oil and gas, coal, phosphorites, zeolites, evaporites, bauxites, ferromanganese, copper ores, placer minerals, and some rare and dispersed elements are associated with limnogenic complexes of different ages. The authors show that a greater variety of minerals of ancient lacustrine complexes compared to modern ones is associated both with variations of lacustrine lithogenesis in the past and with post-sedimentation transformations of sedimentary matter. A particular note is taken about the epigenetic enrichment of ancient lacustrine complexes with ore components. Hydrocarbons and diatomites of lacustrine genesis are of a higher quality compared to similar minerals of marine genesis. The evolutionary changes in the processes of accumulation of limnogenic minerals have affected biogenic and chemogenic components to a large extent. An example of this is the progressive accumulation of caustobiolites and the sulfate evolution of evaporites in lacustrine structures during the Phanerozoic age. An analysis of the genetic characteristics of lacustrine minerals makes it possible to develop new exploratory traits of some sedimentary deposits. © 2022 Institute of Physics Publishing. All rights reserved.