The chemical composition, distribution, and abundance of physiological groups of bacteria in thermal waters and microbial mats formed in the Nachikinsky, Malkinsky, and Verkhne-Paratunsky springs were studied. The degree of accumulation of microelements and formation of minerals by microbial mats of Kamchatka’s thermal springs was also analyzed. The study shows that the waters are characterized by different chemical composition, temperature, and pH content. The thermal waters under study show a low composition and numbers of functional groups of bacteria with the predominance of thionic bacteria. Prevalence of saprophytic, thionic, sulfate-reducing, manganese-oxidizing, ammonifying and nitrifying microorganisms in microbial mats was registered. The relevance of formed microbial mats in the concentration of many heavy metals, alkaline and alkaline earth elements was shown. Thus, cobalt, vanadium, arsenic (Nachikinsky), beryllium, cobalt (Malkinsky), cobalt and scandium (Verkhne-Paratunsky) were most concentrated in microbial mats of Kamchatka’s hydrotherms. All studied microbial communities show the lowest accumulation of Li (1.17-2.22), Sr (2.11-2.79), Rb (2.61-3.12), Cs (2.88-2.98) and As (1.98-2.58). The formation of minerals was found in algo-bacterial mats: quartz, plagioclase, anorthite, calcite, and magnetite.