This paper presents the results of novel field campaigns in the extensive (447,000 km(2)) Selenga River basin, through which 304 samples of river water and 308 samples of suspended matter were collected during high and low water periods between 2011 and 2013. The Selenga River is the largest tributary (more than 50% of the inflow) to the Lake Baikal. Due to ongoing hydroclimatic change and human pressures under conditions of economic growth, the rivers of the area experience significant change in water quality. A key issue for improved understanding of regional impacts of the environmental change is to disentangle the influence of climate change from that of other pressures within the catchment. Our research aims to evaluate the pathways and mass flows of heavy metals and metalloids both in dissolved and suspended forms, taking a basin- scale perspective that previously has not been fully pursued in the Lake Baikal region. Results showed quality deterioration over short distances due to strong impact of hot spots from urban and industrial activities, including mining. The determined enrichment of dissolved metals in waters of Selenga River as well as the spatial and temporal variability of water and suspended sediment composition is further analyzed in the context of climatic, hydrological and land use drivers.