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Fine-grained sediments constitute a major stressing factor for the aquatic ecosystem in the 15000 km2 Kharaa River catchment in Northern Mongolia. The objectives of this study were to identify the suspended sediment (SS) sources and quantify the sediment budget of the basin. Sediment sources were identified with the help of sediment tracing methods utilizing Be-7, Cs-137 and Pb-210 radionuclides. High-resolution discharge data were used in combination with daily suspended solid measurements to calculate the SS budget. These calculations were compared with the monthly archive data on SS and discharge to investigate temporal load variations. In addition, the sediment budget model SedNet was used to estimate the SS budget and test its applicability in a cold semi-arid region. Results of the sediment tracing showed that riverbank erosion generates 74.5% of the suspended sediment load, whereas surface erosion contributes 21.7% and gully erosion only 3.8%. In the most intensely used agricultural tributary catchment Zagdelin Gol, upland erosion contributed only 12.7% to the total SS losses. The calculated mean annual sediment load for the years 19902002 was 20.3 kta1. The SedNet model computed SS export from the catchment in the same order of magnitude as measured data (16.2 kta1). The results help to identify effective management measures to reduce sediment loads and mitigate its impact on the aquatic environment. Copyright (c) 2012 John Wiley & Sons, Ltd.