Since 2003, Limnological Institute SB RAS has been holding the International Baikal Microbiological Symposia “Microorganisms and Viruses in Aquatic Ecosystems” every four years, and even in the “covid” year 2020, it was held “in remote mode.” The proper functioning of viral and bacterial communities is the basis for the stable quality of aquatic ecosystems. New ecological problems for the Lake Baikal ecosystem are becoming more and more acute, and the scientific research, the results of which are presented and discussed at these symposia for different aquatic ecosystems around the world, should help to find solutions for preserving the water quality now and in the future. We analyze the long-term microbiological studies of the water quality in the littoral and pelagic zones of Lake Baikal carried out by numerous authors, and propose a specific scheme of microbiological monitoring of this unique aquatic ecosystem required by the environmental regulatory authorities. Specific measures to prevent pollution of oligotrophic lake waters are also provided; these measures can be rapidly implemented now.