In hygrothems of Central Mongolia the physical-chemical parameters of water and bottom sediments were investigated and rates of microbial production and destruction processes were determinated. Temperature of thermal waters reached 45–90 °С, pH equally 8,5–10,4, the hydrogen sulfide maintenance makes 0,5–15 mg/dm3. Microorganisms were formed cooperative alkalothermophilic community. At high temperatures and alkaline рН in various types of hydroterms they effectively carry out processes of production and destruction organic substance, transformation volcanic fluids and synthesis of biogene minerals.