Although metallic mineral resources are most important in the economy of Mongolia, mining activities with improper management may result in the pollution of stream waters, posing a threat to aquatic ecosystems and humans. In this study, aiming to evaluate potential impacts of metallic mining activities on the quality of a transboundary river (Selenge) in central northern Mongolia, we performed hydrochemical investigations of rivers (Tuul, Khangal, Orkhon, Haraa, and Selenge). Hydrochemical analysis of river waters indicates that, while major dissolved ions originate from natural weathering (especially, dissolution of carbonate minerals) within watersheds, they are also influenced by mining activities. The water quality problem arising from very high turbidity is one of the major environmental concerns and is caused by suspended particles (mainly, sediment and soil particles) from diverse erosion processes, including erosion of river banks along the meandering river system, erosion of soils owing to overgrazing by livestock, and erosion by human activities, such as mining and agriculture. In particular, after passing through the Zaamar gold mining area, due to the disturbance of sediments and soils by placer gold mining, the Tuul River water becomes very turbid (up to 742 Nephelometric Turbidity Unit (NTU)). The Zaamar area is also the contamination source of the Tuul and Orkhon rivers by Al, Fe, and Mn, especially during the mining season. The hydrochemistry of the Khangal River is influenced by heavy metal (especially, Mn, Al, Cd, and As)-loaded mine drainage that originates from a huge tailing dam of the Erdenet porphyry Cu-Mo mine, as evidenced by δS values of dissolved sulfate (0.2 to 3.8 ‰). These two contaminated rivers (Tuul and Khangal) merge into the Orkhon River that flows to the Selenge River near the boundary between Mongolia and Russia and then eventually flows into Lake Baikal. Because water quality problems due to mining can be critical, mining activities in central northern Mongolia should be carefully managed to minimize the transboundary movement of aquatic contaminants (in particular, turbidity, dissolved organic carbon, Fe and Al) from mining activities.