The discrepancy between the boundaries of river basins, within which pollutants are transported by water flows, and the administrative (municipal) districts where their sources of entry into rivers are located, is a complex scientific and methodological problem of water resources management. The article presents an integrated assessment of anthropogenic impact calculated using state statistics for municipalities of the Baikal natural territory. Using the example of river basins—tributaries of Lake Baikal located within its boundaries—the authors discuss the proposed methodology for assessing the contribution of municipalities to the inflow of heavy metals and metalloids (V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Cd, Pb, Mo, P, Sb, Sn, U) in dissolved and suspended form with river flow into Lake Baikal. The methods of regression analysis have determined the leading role of 5 impact factors statistically influencing the formation of concentrations and flows of priority pollutants in the closing channels of 13 major tributaries of Lake Baikal (Selenga, Barguzin, Turka, Tyya, Verkhnyaya Angara, Snezhnaya, Kicher, Goloustnaya, Buguldeika, Utulik, Kika, Frolikha, Bolshaya Cheremshana rivers). These include: the volume of wastewater discharge; the volume of untreated wastewater discharge; areas disturbed by mining activities; the geomorphological hazards of the territory; the rate of potential soil erosion. Taking into account individual municipalities located within river basins in the formation of the total impact for each of the five factors allowed us to justify a method for determining the quantitative role of municipalities in the formation of the flow of pollutants. Within the boundaries of the Baikal natural territory, the level of anthropogenic impact by most indicators shows a slight downward trend with an increase in the localization of pollution in three urban agglomerations (from 10 to 30% for each of the substances in the Ulan-Ude urban okrug, Severobaikalsky and Selenginsky municipal districts). This zone is characterized by the highest wastewater load in relation to the volume of surface water.