Regions of the Russian Federation classified among Arctic zone estimated to 22% of Russian territory. Arctic is characterized by the richest reserves of natural resources, and its phased, balanced development is the most important strategic task of Russia’s socioeconomic development. Production and household activities of the population of Russia living and working in the far North is associated with difficult climatic and geographical conditions. In this case, the constant cold and consumption of contaminated water can lead to aggravation of various human disease. The Arctic zone of the Russian Federation is characterized by the richness of water resources as rapidly renewable (river runoff and its underground component), and static one to which are assigned the waters of lakes, underground waters, waters (ice) of mountain and polar glaciers. A characteristic feature of water consumption in the Arctic regions is the active use of lake water, which in a number of settlements is the main source of drinking water supply. In this regard, the assessment of the lake’s fund of Arctic zone and its ecological status is extremely topical.According to the assessments, more than 2.5 million water bodies, that is a ~2/3 of all water bodies of the country, are decoded in the Arctic zone of the Russian Federation on satellite images. Mainly, these are small water bodies, only about 975 thousand of them exceed 1 ha. The total area of the water surface of Arctic lakes is ~160 thousand km2 (slightly less than a half of the total water surface of all natural water bodies of the Russian Federation), and the total volume of water enclosed in them is ~760 km3.Even in the middle of the 20th century, the lakes of the Russian Arctic, with rare exceptions, were characterized by the highest quality of their waters, but by now the ecological status of many water bodies has deteriorated significantly. The vulnerability of Arctic lakes to pollution is enhanced both by virtue of the peculiarities of their orometry and by the simplicity of the biological communities of northern ecosystems characterized by a low degree of stability. The poor knowledge of Arctic water bodies does not allow taking the necessary preventive measures for their protection and rational use. In this connection, attention to the expansion of works on the integrated study of limnology of water bodies included in the lake fund of the Arctic zone should be paid.An estimation of water resources of lakes of the Arctic zone of Russia, their ecological status and the questions of etiology of diseases on the territories of the Far North are given in this article. The morbidity of the population of the Arctic regions of Russia today is much higher than the national average. Further development of the territory and the observed warming of the climate will lead to increasing pollution of freshwater resources with toxic substances, pathogenic microorganisms and viruses. This will exacerbate the issue of ensuring environmental safety and meeting the needs of the population in quality drinking water. The situation is further aggravated by the fact that the most affordable technologies for water treatment and wastewater treatment in conditions of low temperatures and high content of humic substances in the initial water cannot ensure the proper level of disinfection. In this regard, one of the topical issues is the creation of innovative technologies for water purification that are more adequate to the conditions of the Arctic zone of Russia.