The main territory of Azerbaijan Republic is situated within arid climate and vast majority of the water resources are involved in the national economic production. Approximately 70% of the water resources are from the transboundary rivers. In states with a current 30% and, as was estimated, more than 40% in the near future deficit of general water resources, the optimal use of fresh surface and groundwater resources great significance and strategic importance for economy of the new independent country in the current situation. As a result, the stress of the potable water resources in various sectors of the national economy, especially in agriculture, which is a major hazard of the countries’ food security. This is the reason that currently the interest in the impacts of climate change on water resources in the Republic has developed greatly. The research data demonstrate that the water resources formation in Azerbaijan are very depend on the climate components and highly sensitive to variations in climate. At a time when over the whole territory of the Republic natural conditions are not co-operated to form the potable water resources and other analyses suggest that groundwater resources and water quality could all be significantly affected by climate change over the course of the coming decades. It may be very important factor against sustainable development of Azerbaijan. This paper examines the scientific and technical aspects of evaluating the state of affairs of the water resources management, risk assessment and their degree of vulnerability due to consequences of climate variation in the Republic of Azerbaijan.