A striking feature of the Mongolian plateau is the wide range of air temperatures during a year, -30 to 30°C. High summer temperatures, atmospheric weathering and the arid climate lead to formation of numerous alkaline soda lakes that are covered by ice during 6–7 months per year. During the study period, the lakes had pH values between 8.1 to 10.4 and salinity between 1.8 and 360 g/L. According to chemical composition, the lakes belong to sodium carbonate, sodium chloride-carbonate and sodium sulfate-carbonate types. This paper presents the data on the water chemical composition, results of the determination of the rates of microbial processes in microbial mats and sediments in the lakes studied, and the results of a Principal Component Analysis of environmental variables and microbial activity data. Temperature was the most important factor that influenced both chemical composition and microbial activity. pH and salinity are also important factors for the microbial processes. Dark CO2 fixation is impacted mostly by salinity and the chemical composition of the lake water. Total photosynthesis and sulfate-reduction are impacted mostly by pH. Photosynthesis is the dominant process of primary production, but the highest rate (386 mg C/(L∙d)) determined in the lakes studied were 2–3 times lower than in microbial mats of lakes located in tropical zones. This can be explained by the relatively short warm period that lasts only 3–4 months per year. The highest measured rate of dark CO2 assimilation (59.8 mg C/(L∙d)) was much lower than photosynthesis. The highest rate of sulfate reduction was 60 mg S/(L∙d), while that of methanogenesis was 75.6 μL СН4/(L∙d) in the alkaline lakes of Mongolian plateau. The rate of organic matter consumption during sulfate reduction was 3–4 orders of magnitude higher than that associated with methanogenesis.