The article discusses issues of Russian sovereignty over transboundary rivers. It reveals that in accordance with the UN Charter and international treaties, states have full sovereignty over their natural resources. As to environmental protection against transboudary pollution and damage and also in relation to the use of shared natural resources, international law applies this principle in combination with the principle of limited sovereign rights. In conformity with the intergovernmental water basin agreements of Russia with the watershed countries the external involvement into the national decision-making process is carried out through mutual commitments and obligations to recover the environmental damage, conducting joint monitoring, notification about on-going and planned activities that have or may have negative impacts on a transboundary river, related water uses and facilities, division of a water flow, joint inspections and agreed exploitation of hydrotechnical objects. Application of the limited sovereign rights to shared water resources has an objective nature-based rationale – ecosystem integrity of a shared water body, that justifies and ensures its protection against degradation, equitable and reasonable utilization by coastal states.