Hydropower development causes a multitude of negative effects on freshwater ecosystems, and to prevent and minimize possible damage, environmental impact assessments must be conducted and optimal management scenarios designed. This paper examines the impacts of both existing and proposed hydropower development on the transboundary Amur River basin shared by Russia, China, and Mongolia, including the effectiveness of different tools and measures to minimize damage. It demonstrates that the application of various assessment and conservation tools at the proper time and in the proper sequence is the key factor in mitigating and minimizing the environmental impacts of dams. The tools considered include basin-wide assessments of hydropower impacts, the creation of protected areas on rivers threatened by dam construction, and environmental flows. The results of this work show how the initial avoidance and mitigation of hydropower impacts at early planning stages are more productive than the application of any measures during and after dam construction, that the assessment of hydropower impacts must be performed at a basin level rather than be limited to a project implementation site, and that the full spectrum of possible development scenarios should be considered. In addition, this project demonstrates that stakeholder analysis and robust public engagement are as crucial for the success of environmental assessments as scientific research is for the protection of river basins.