Comprehensive studies of soil contamination were performed in the area of settlement Kichi-Kemin (Kyrgyz Republic). Soils of the Kyrgyz Republic are exposed to waste (tailings) of many industrial enterprises of the mining industry not far from the village of Ak-Tuz, located 145 km from the capital of Kyrgyz Republic, Bishkek, at an altitude of 2300 m above sea level. It is noted that 4.17 million tons of radioactive waste from one of the enterprises were once disposed of at four tailings in the Kichi-Kemin Valley. The main waste elements are radioactive thorium, heavy metals such as cadmium, molybdenum, lead, zinc, beryllium, and oxides of hafnium and zirconium. The impact of these wastes on soil ecotoxicity and microbial communities is not yet well understood. In this work, soil environmental assessment near waste deposits were investigated using an integrated method known as the Triad approach. The integral index of soil disturbance was calculated from the data of ecological observations of soil microbial communities (bioindication), data of ecotoxicological index by phytotesting approach (bioassay), and chemical index reflecting the results of a quantitative chemical analysis of the content of pollutants. The ecological index, calculated from the bioindication parameters of the soil microbiota communities, has become a reputable indicator of the state of soils from vulnerable mountain ecosystems. Studies of soil microorganisms have shown a decrease in species diversity in contaminated soils. The most resistant species of fungi were Aspergillus and Penicillium. Among the actinomycetes of the genus Streptomyces, the Albus and Cinereus sections proved to be stable. Estimation of anthropogenic impacts on mountain ecosystems in the Kyrgyz Republic using the Triad approach has shown that the most sensitive toxicity index in the soils of the Ak-Tuz is the ecotoxicological indicator EtoxRI; determined by the phytotesting method. The integrated index calculated on the basis of the Triad method gave a more complete picture of the influence of pollutants on the soils ecosystem of the Ak-Tuz, characterizing its severe deterioration.