The Selenga River Basin (Mongolia and Russia) has suffered from heavy metal contamination by placer gold mining and urban activities in recent decades. The objectives of this study were to provide the first distribution data of dissolved organic matter (DOM) and humic substances (HS) in this data-scarce region, and to investigate their association with dissolved and colloidal metals. Two sampling campaigns were conducted in August of 2013 and 2014. A constant proportion of HS (%HS; coefficient of variation of 2%) was observed from the headwater of Tuul River to the end of the delta before Lake Baikal, spanning > 1000 km in distance. The relationships were determined as HS = 0.643 × DOM ( R 2  = 0.996, P  < 0.001), and this value (%HS = 64.3) is recommended as an input parameter for metal speciation modeling based on samples collected from the rivers. The DOM and metal (Al and Fe) concentrations in samples doubled through the Zaamar Goldfield mining area, but the influence was mitigated by mixing with the larger Orkhon River, which has better water quality. Metals were mainly present as colloids and had a strong positive correlation with DOM (Al r  = 0.81, P  < 0.01; Fe r  = 0.61, P  < 0.01), suggesting that DOM sustains colloidal Al and Fe in solution and they are co-transported in the Selenga River Basin. Land use changes affect water quality and metal speciation and therefore have major implications for the fate of metals.