The purpose of the presented study is to develop a methodology for assessing the anthropogenic impact on the environment in the municipalities of the Baikal Natural Territory (BNT) and applying the obtained methodology to the studied territory. The article analyzes the existing methodological approaches to the assessment of anthropogenic impact on the environment. To carry out a comprehensive integrated assessment, the authors proposed an algorithm for calculating the anthropogenic impact index based on 22 indicators integrated into 7 subindexes (impact on the atmosphere, water and forest resources, agricultural impact, solid waste, disturbed lands and objects of accumulated harm, as well as background impact).The weight of the indicators was determined by interviewing experts representing the scientific community (leading experts in the field of integrated assessments of certain types of impacts or specialists in the field of environmental problems of the BNT), the expert community (leading analytical agencies developing environmental ratings), as well as the environmental management system of the regions included in the BNT. The inertial nature of the anthropogenic impact characteristic of municipalities within the boundaries of the BNT, as well as the general tendency to reduce the impact, has been revealed. At the same time, the absence of positive changes in the environmental state was noted, especially characteristic of the largest impact centers with their inherent unfavorable environment, which suggests the need to take measures to reduce the impact. The advantage of the methodology proposed by the authors can be considered the possibility of extending monitoring in the future, which opens up the possibility of using this algorithm to assess the environmental situation and form environmental policy priorities. The analysis of the results confirmed the quality of the integrated assessment methodology and showed that the districts, cities and towns of the BNT are highly polarized in terms of the level of anthropogenic impact concentrated in certain areas, primarily in the zone of atmospheric influence. The main strengthening of the AI is characteristic of municipalities located along transport corridors, the axis of which is the Trans-Siberian Railway, The Baikal–Amur Mainline and the «Power of Siberia» gas pipeline.