The relevance of the work is caused by the need to establish special land use conditions within the zones of sanitary protection and third zones according to the existing standard regulations. At the same time, natural hydromineral complex, in certain conditions, has the ability to delay and decompose pollutants, allowing the pollutants to migrate over significant distances. After necessary research, the size of the sanitary protection zones can be reduced to the minimum necessary without compromising safety of operation of water intakes. This is highly relevant to human settlements on the territories with are groundwater intakes. The aim of the research is to determine the true dimensions of the boundaries of sanitary protection zones of groundwater intakes considering the capacity of hydromineral complex to prevent the migration of contaminants from surface sources of pollution in aquifers and complexes. Methods: laboratory determination of mineralogical composition, total content of organic substances and protein, determination of absorption capacity and composition of the exchange complex, composition of pore solutions and readily soluble salts, total content of phosphorus and arsenic in the rocks of aeration zone and water-bearing rocks and chemical composition of groundwater, including trace components. Laboratory studies of direction and intensity of microbiological processes. Results. The authors made a conclusion on freezing by geological medium the pollutant distribution from surface sources in the immediate vicinity of the sources; defined the capabilities of natural microbiat populations in degradation of organic pollutants. It is recommended to determine on-site the Susunaiski artesian basin the boundaries of sanitary protection zones of the second and the third belts within the boundary of sanitary protection zone of the first belt.