The analysis of experimental data obtained from studying the ecological-microbiological and biochemical characteristics of soil cover in the influence area of emissions from East Siberia’s aluminum smelters was performed. It is found that actinomyces and chemoorganotrophic non-spore-forming eubacteria undergo the most severe inhibition under the influence of the water-soluble form of fluorine (10–20 MPC in the 0–10 cm layer) in the anthropogenically transformed sod forest soil of the subtaiga zone. A decline of the level of biochemical activity is observed in humus-deficient chernozem of the steppe to be caused by fluorine (1–4 MPC in the 0–10 cm layer).