Mineral lakes with elevated water mineralization (of the order of 10 or 100 g/l) that contain natural brine and therapeutic mud occupy a prominent place among the natural recources of Siberia. All told, there are about one thousand mineral lakes in Siberia (East and West altogether). They are best studied in the most populous southern Siberia, but in spite of certain success they are still poorly studied. Nevertheless, nowadays it is time to consider new problems related to the protection of mineral lakes in Siberia, many of which are unique in their chemical composition and balneological effect. These lakes are located not only in the areas of Siberia with insufficient humidification (the Kulunda Valley, Altai Territory, Hakassia, and Tuva), but also in Transbaikalia. So, in the Chita Region there are 85 mineral lakes with water table surface exceeding 0.1 sq. km, and more than 20 in Buryatia. They also occur in Yakutia, the region of permafrost rocks (e.g. Lake Anger-Dirinae in Central Yakutia, with the total surface of about 150 thousand sq. km). Here, they are not investigated, but are renowned among the population). Although there are health resorts on some lakes, their mineral resources are not adequately utilized. Mud, brine and mineral water cure started on Siberian mineral lakes a century ago. The procedures for using these substances are well known. Presently, extensive use is being made of the newly discovered therapeutical groundwaters on the lakes where medical centers have been founded. On the examples of lakes Shira, Tagarskoye, and Uchum (south of the Krasnoyarsk Territory), the authors discuss the rise and organization of medical institutions on Siberian mineral lakes, their water regime and balance, the long-term regularities in the development of therapeutic properties of mud and water, the current status of lake protection and the necessary arrangements, types and sources of pollution, the prospects for future development and utilization of the lakes.