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Lake Baikal receives water from the rivers draining vast transboundary area in the Northern half of Mongolia and Southern Siberia. The watershed covers both large areas of pristine steppe and forest, but also several urban centers (including the Mongolian capital of Ulaanbaatar and the Buryatian capital of Ulan Ude) and mining areas which are important sources of pollution. Moreover, environmental legacies related to past mining and industrial activities continue to emit pollutants to the aquatic environment. The study provides integrated assessment of urban impacts on water and sediment quality based on unique monitoring network since 2011 containing over 100 stations over Baikal Lake catchment focusing on over 70 chemical compounds at both pollution sources and most downstream locations near Lake Baikal. Climate change, land use changes, general socio-economic developments (e.g. regarding population or mining) are considered as main contributors to pollution spreading. The results indicate particular role of urban areas in aquatic system pollution by heavy metals and nutrients.