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Since the early 20 century the development of industry has lead to the increase in pollution of underground waters suitable for consumption and domestic needs with toxic metals, radionuclides, nitrogen compounds, pesticides and hydrohalogens substances. Such pollutants are able to migrate with the flow of underground waters for an unlimited period of time and cause toxic effects in people’s organisms. The project meets the objectives of the selected priority, as it affects the comprehensive study of reservoir fluid samples approximately the conserved storage of radioactive waste and also is aimed at reducing the risks of spreading the migrable toxic waste components. The aim of this work is to find and study the properties of natural materials and their modifications, as well as the features of them biofilm with microorganisms of different physiological groups and assess their metabolic capacity to establish biogeochemical permeable (reactive) multifunctional barrier in the underground waters, preventing the spread of radionuclides (U, Tc, Pu) of heavy metals (Cd, Cr), and nitrate ions. Materials such as naturally occurring zeolite, shungite, perlite and vermiculite and their modifications were studied. Distribution coefficients (Kd) and desorption rate for radionuclides and this materials due to geochemical characteristics of natural waters were obtained. High effective stains of microorganisms (Pseudomonas veronii, Pseudomonas mandeli, Pseudomonas asplenii, Pseudomonas putida, Shewanella putrefaciens, Shewanella putrefaciens, Shewanella xiamenensis, Shewanella oneidensis, Pantoea agglomerans) isolated from radionuclides contaminated aquifers, with ability to reduce metals from higher oxidation state and nitrate to molecular nitrogen were found. Biocompatibility of this microorganisms and inorganic materials and ability to form biofilms on such mineral porous materials were investigated. We found high efficiency of shungite for pertecnetate and zeolite for uranyl removal. It was found that microorganism where able to form stable biofilms on minerals surface and cause uranium, technetium and chromium and nitrate reduction due to cell respiration processes in anaerobic conditions. In lab modelling experiments with natural microflora of subsurface water samples from polluted with nitrate ions horizons we found high levels of nitrate reduction to molecular nitrogen and Eh decreasing from +120-150 to -60 - -80mv which also can cause metal immobilization in lowest oxidation state.