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The Selenga River, which originates in Mongolia, contributes about 50 % of the total inflow into Lake Baikal. Together with the Angara and Yenisey rivers it forms the longest river network in Eurasia. Mining, industrial and agricultural activities within the Selenga drainage basin affect the sediment influx and transport along the river and its tributaries. Novel screening campaigns were conducted in June–August 2011-2012 in both the Russian and the Mongolian parts of the Selenga river basin. Discharge and suspended sediment concentration (SSC) data were combined to yield estimates of daily and monthly water discharges, suspended load averages at more than 150 locations. The chemical analysis of large number of chemical elements (heavy metals et al.) in water, sediments (riverbed and suspended) and aquatic plants was done mainly by ICP method. The conducted monitoring and modeling characterize the spatial variations of suspended load and its characteristics (SSC, grain size, organic matter content) over river basin in the summer season. The increasing human activities (mining and pastures) increases the portion of fine-grained clay particles in total sediment load. Both empirical data and modeling results showed that flow peaks carry very high sediment loads. The main sources of sediment pollution of Selenga River are related to industrial and mining centers. The population of Ulaanbaatar city exceeds 1 million. The technogenic geochemical specialization of the city is derived from many different pollution sources which release Ag, Pb, Sn, Hg, Ge, Zn, and W. The widest spectrum of HMs was found in the soils of many-storied residential areas and near the major highways. The geochemical specialization of Darkhan city is the result of Cr, Hg and W contamination produced by leather tanning, gold mining and thermal power plants. Although its population is 10 times less than in Ulaanbaatar the industrial zone of Darkhan city is characterized by HMs anomalies of very high magnitude. The mining activity disturbs the natural sediment transport regime, and has impact on the erosion-deposition patterns, especially during high flow conditions. The study revealed rather high levels of dissolved Fe, Al, Mn, Zn, Cu, and Mo in the Selenga River water which often are higher than MPC for water fishery. Most contrast distribution is characteristic for W and Mo, which is caused by mineral deposits in the Selenga basin. The most severe pollution of aquatic systems in the basin caused by mining activities is characteristic for a small river Modonkul, which flows into Dzhida River (left tributary of Selenga). Reported multi-decadal declines in sediment fluxes in the downstream Selenga river can be attributed to the abandonment of cultivated lands and (most likely) to changing hydroclimatic factors, such as in particular decreasing water flows due to reduced precipitation and intensified water use for irrigation purposes. The main output of the work is that the rapid urbanization and clear cutting of forests, open gold- and other metal-mining activities that are typical for Central Asia have a profound impact on water, suspended sediment load and water quality of the Selenga River.