Even though the Selenga is the main tributary to Lake Baikal in Russia, the largest part of the Selenga River basin is located in Mongolia. It covers a region that is highly diverse, ranging from almost virgin mountain zones to densely urbanized areas and mining zones. These contrasts have a strong impact on rivers and their ecosystems. Based on two sampling campaigns (summer 2014, spring 2015), we investigated the longitudinal water quality pattern along the Selenga and its tributaries in Mongolia. While headwater regions typically had a very good water quality status, wastewater from urban areas and impacts from mining were found to be main pollution sources in the tributaries. The highest nutrient concentrations in the catchment were found in Tuul River, and severely elevated concentrations of trace elements (As, Cd, Cu, Cr, Fe, Mn, Ni, Pb, Zn), nutrients (NH₄⁺, NO₂⁻, NO₃⁻, PO₄³⁻), and selected major ions (SO₄²⁻) were found in main tributaries of Selenga River. Moreover, trace element concentrations during spring 2015 (a time when many mines had not yet started operation) were markedly lower than in summer 2014, indicating that the additional metal loads measured in summer 2014 were related to mining activities. Nevertheless, all taken water samples in 2014 and 2015 from the main channel of the Mongolian Selenga River complied with the Mongolian standard (MNS 1998) for the investigated parameters.