Contemporary challenges and threats to sustainable development including safe use of transboundary resources of rivers and Arctic seas in condition of climate change are connected with cumulative impact of numerous factors. Ongoing environmental changes have transboundary nature and will have significant impact in international scale. In case of overlapping of factors of impact their nature and synergetic effect, mechanisms of their interrelated influence and possible negative consequences for global economy, environment and human health are not adequately known. Among the main obstacles to mitigation of climate change impact on the state of big river basins in the Arctic and Arctic seas are: the lack of critically important information and data, absence of modern concepts of climate change mitigation measures connected with impact on Arctic seas, uncoordinated and inefficient regulation and management, absence of unified interstate tools of marine spatial planning. The article contains the analysis of risks and global consequences of the ongoing climate change for water resources; characteristic of priority issues and their underlying root causes. It also contains the results of the analysis of risks connected with melting of permafrost and increase in thermal coast erosion, assessment of the role of transboundary cooperation of water issues for sustainable regional development. The authors also propose some measures for addressing the above issues based on the Strategic Programme of Actions on the Protection of the Russian Part of the Arctic developed by the Ministry of Economic Development of Russia.