The aim of the study was to develop a scientific and technical justification for the bioconversion of bottom sediments using mesophilic prokaryotes. The main component of the bottom sediment bioconversion technology includes microorganisms of the genus Bacillus spp., isolated in a pure culture from the microbial community of bottom sediments. Bacilli are highly resistant to natural (climatic) conditions, anthropogenic factors, elevated concentrations of pollutants and are able to adapt to their effects. As a result of the laboratory experiment, work was carried out on the selection of factors that ensure the intensity of microbial bioconversion of bottom sediments. In order to achieve the maximum effect from the enzymatic and biochemical activity of bacilli, kinetic characteristics associated with the achievement of maximum values of optical density, microbial cell concentration and growth rate were studied. After analyzing a number of the above indicators, it is concluded that the method of processing bottom sediments using mesophilic prokaryotes of the genus Bacillus spp. will allow in the future to obtain an environmentally friendly and mineral-saturated product for further use in the practice of crop production.