The aim of the study is a comprehensive assessment of the state of natural-territorial complexes of the Baikal State Natural Biosphere Reserve, including an ecological and geochemical assessment of soils, analysis of plant communities, determination of the ecological and biogeochemical features of the vegetation of the area. The distribution of mobile forms of heavy metals in the soils of the Baikal Biosphere Reserve has been studied. The coefficient of total soil pollution has been calculated. The maximum allowable concentrations exceedances for Cr, Mn, Cu and Pb were registered. Analysis of the microelement composition of the crust of Pinus sibirica showed the accumulation of Cd and Ni in relation to the Dobrovolsky clarke in all the studied areas of the reserve. Based on the studies carried out, it can be recommended to monitor the ecological state of natural territorial complexes on a regular basis on the territory of the Baikal State Biosphere Reserve.