Background: Mongolia is characterized by restricted sources of drinking water and intensive water pollution due to high rates of urbanization, mining industry development, enormous amount of livestock, and ever-growing attempts in domestic production of cereals and vegetables. Among others, Se is the least studied element in Mongolian water resources. Goal: To assess the selenium content of Mongolia’s drinking water depending on its geographical location and to identify areas of environmental risk associated with the chemical composition of the water. Materials and Methods: In the summer of 2017, water samples were collected from 5 aimags (Dornogovi, Tuv, Selenge, Umnugovi, Arkhangai) and Ulaanbaatar city and sent to Moscow, Russia for analysis. Of the collected samples, 19 were groundwater (wells, wells, springs) and 2 were surface water (Tuul River, Selenge River). Results: Based on fluorimetric method of analysis, the first results on Se levels in drinking water of five aimags, Ulaanbaatar, and Erdenet were obtained. Uneven distribution of Se in Mongolia was manifested, the highest Se concentrations being typical for the southern resources (up to 18,600 μg/L) and the lowest, for the Northern ones (up to 0.022 μg/L). ICP-MS data of Al, As, B, Ca, Cd, Co, Cr, Cu, Fe, Hg, I, K, Li, Mg, Mn, Na, Ni, P, Pb, Si, Sn, Sr, V, and Zn contents indicate poly-microelementosis existence in the South of Mongolia (Dorno-Gobi aimag) where ground water is characterized by elevated levels of As and extremely high levels of Se, Li, Na, F, Cl, B, and nitrates ions, exceeding maximum permissible levels by 1.86; 4.3; 3.1; 3.1; 2.7; 3.4; and 1.8 times respectively. Toxic concentrations of Se in groundwater of Dorno-Gobi aimag contradict with the published low human serum Se and low content of the element in horseflesh that suggests the possible effect of the above pollutants on Se bioavailability. Conclusion Revealed phenomenon and mosaic distribution of heavy metals in areas with high and low Se content in water resources indicate the need of direct search for Se and other pollutant transfer in food chain in various ecological loading conditions, creation of a map of Se distribution in water resources of other Mongolian regions, and large-scale evaluation of the human poly-elemental status.