To date, considerable experience has been accumulated in assessing and standardizing the quality of natural waters, however, the role of regional factors in practical standardization in most cases is ignored. Due to the lack of recommendations for establishing permissible loads on a water body, taking into account its natural characteristics, the effectiveness of water protection measures is reduced. Determination of the concentrations of pollutants using maximum permissible concentrations without taking into account the hydrological and hydro/chemical characteristics of water bodies does not ensure the environmental safety of the water body. The regulation of the water quality of water bodies must necessarily reflect the regional features of the formation of the chemical composition of natural water in a particular territory, since the soil and geochemical features of the catchment area of the basin reflect natural background concentrations. Methods. The article proposes a new approach to assessing the qualitative determination of priority pollutants taking into account the regional background. For a qualitative assessment of the level of natural content of dissolved forms of heavy metal compounds, statistical processing was carried out for the main phases of the water regime. The significance of the difference between the sample of summer samples of river water for pollutants from the corresponding sample of winter samples and rainwater samples was determined using the Wilcoxon-Mann-Whitney nonparametric statistical test. Results. The proposed approach for statistical processing of long-term data enables to make qualitative assessment of the natural level of the content of heavy metal compounds on the surface and in the strata of soils that compose the basins of the Malka, Urukh, Cherek, Chegem rivers. The results obtained can be used to improve the methodological and practical issues of regionally oriented standardization.