This article describes crystallization formed in the exogenous mucous sheath of phototrophic microorganisms living in the surface waters of the south area of the Komi Republic. The mineralization of colonies of cyanobacteria of the Gloeotrichia sp. and green algae Chaetophora elegans was studied. The waters of rivers in the Northern Dvina basin have been studied as habitats for the microorganisms. They have a different composition: HCO3 Ca–Mg, typical for the taiga zone of a temperate continental climate; SO4–HCO3 Ca–Mg and Cl–Na (in the zone of technogenic pollution). Using the example of these neutral — weakly alkaline ultrafresh — salty (0.2—2.8 g/L) waters, it is shown that the geochemistry of the aquatic environment is one of the most important factors influencing the minerogenesis. Calcite, vaterite, quartz and halite were identified in dried colonies of microorganisms within the extracellular polymeric substance using the methods of X-ray diffractometry, electron microscopy, microprobe analysis and IR spectroscopy. The morphological features of microminerals are presented depending on the type of microorganisms. Calcium carbonate crystals and aggregates are formed within the exogenous mucous sheath of algae and cyanophytes. The carbon isotope composition of carbonates (13C –7.5 and –3.8 ‰ PDB) indicates their organic nature. The formation of minerals, morphological features of crystals and the degree of biomineralisation of colonies of phototrophic microorganisms are conditioned by the physicochemical parameters of the aquatic environment. The possibilities of chemogenic precipitation of carbonates from the studied natural waters were assessed.