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Gathering the efficient information on water-related hazards of transboundary river systems remains the crucial task in international water management, environmental pollution control and prevention health problems. Countries, located in the low parts of the river basins, depend on the water strategy and water use in the adjacent countries, located upstream. Surface water pollution is considered to be the most serious problem, facing the above-mentioned countries. Large efforts in terms of field measurement campaigns and (numerical) transport modeling are then typically needed for relevant pollution prediction and prevention. Russian rivers take inflow from 8 neighboring countries. The transboundary river system of Selenga and Amur river which form the Eastern border of Russian border are particularly challenging. The first is the biggest tributary of Lake Baikal which is the largest freshwater reservoir in the world. Selenga River contributes about 50 % of the total inflow into Baikal, whereas the last is amont the largest hydrological pathways of Eurasia. The mentioned rivers originate in the mountainous parts of China and Mongolia and then drain into Russia. There are numerous industries and agricultural activities within the Selenga drainage basin that affect the water quality of the river system. The study follows the need to study water-related hazards in these transboundary basin with a particular focus on water quantity and quality, as far as surface water ecology, water use, and integrated management approaches. The preliminary results provide evidence on a connection between increased river pollution and heavy metal concentrations. Pollutant source zones are located mostly at industrial and mining centers, both with huge amounts of material supplied from non-point (diffuse) sources - in-channel erosion and land use. The further work will be devoted to the understanding of matter input into river systems and its qualitative assessment during various water stages. The work more specifically aims at quantifying downstream impacts of various sources based on limited monitoring data, a condition that the presently considered region shares with many fast developing regions of the world. Understanding of diffuse as well as point source zones of matter supply is essential to the knowledge needed for more detailed impact assessments and management decisions, regarding remediation planning and measures. The integrated concept of micro (experimental plots, individual point data), meso (small rivers) and macro (Amur and Selenga River Basin) scales is designed for the interpretation of existing data on floods, surface water quantity and quality in a wider context. On the other hand, it empirically underpins the complimentary character of intensive monitoring in selected model regions with more extensive monitoring in larger areas.