The article is devoted to the study of the transboundary river Yertis, which flows through the territories of China, Kazakhstan and Russia, being an important element of the ecological and geopolitical system. To assess the state of the river's ecosystem, comprehensive research was conducted at 17 control points, including physico-chemical water analysis and modern monitoring methods such as drone aerial photography and bathymetric surveys to build 3D models of bottom. The analysis of water samples from the Yertis River taken near the Pryrechnoye village in Abay district showed a significant excess of maximum permissible concentrations of suspended solids and sulfates by 204 and 1.12 times, respectively, which indicates a significant anthropogenic impact. The analysis of Semey city wastewater, showed that the concentrations of total iron, copper, nickel, and hexavalent chromium in the collected samples do not exceed the maximum permissible limits. The results of aerial surveys and bathymetric analyses revealed the heterogeneity of the river ground, the presence of areas of slow flow and sediment accumulation, and changes in the river channel caused by flooding. With the help of obtained data, it is possible to model hydrodynamic processes, predict floods, and develop measures to minimize environmental risks.