Recently, it has become increasingly important to solve the problems of environmental pollution using ecologically safe processes based on natural mineral and biological components. The paper presents the results of research of shungite rocks of various genesis for use in innovative methods of water purification with the joint use of useful microbiota, effective microorganisms (yeast, lactic acid bacteria, etc.). It is shown that rocks of different stratigraphic levels (second, fourth and sixth), differing in composition and structure, are characterized by different degrees of leaching of chemical elements, sorption activity to cationic and anionic complexes, and are differently able to sorb polluting components from water, including heavy metals. It was found that unmodified shungite rock inhibits the functioning of effective microorganisms in direct contact, and for heat-treated shungite rock, on the contrary, the growth of effective microorganisms is observed.