Abstract— <p>A comparative analysis has been conducted on the distribution of selenium concentrations in the water of the associated media of the Lake Baikal ecosystem (surface and deep water of Lake Baikal, well water on Ol’khon Island and on the lake shore, water from numerous tributaries, cold and hot mineral springs, the source of the Angara River, and snowmelt). The Se indicator role reflects the deficiency of its concentrations in all aquatic components of the environment of the Baikal Region. The selenium content in the Baikal water media varies from 0.01 to 3.1 µg/L. The median values are similar and lie within one or two orders of magnitude. Increased selenium contents are found in the water of wells and cold springs located in the Jurassic coal-bearing rocks and in the subalkaline granitoids of Ol’khon Island. We have established the potential chemical effect of snowmelt on the water at the source of the Angara River resulting in its increased concentrations of Se brought with the snow runoff from industrial areas of the Baikal Region. We believe that the strong continental climate, high seismic activity, and the peculiarities of the water currents in Lake Baikal contribute to the renewal of deep-seated water maintaining its geochemical composition and purity, despite the entry of selenium from man-made sources.</p>