The article considers the controversy over the water sharing in the transboundary river basin Syrdarya, with the particular attention to the Ferghana Valley. The Fergana Valley is an area where almost all the Central Asia’s problems (territorial, ethnic, shortage of water and land resources, etc.) are represented in the most concentrated form. The analysis of the key contradictions of the Ferghana valley is critical to understanding the socio-political situation in the Central Asian region. The article analyzes the formation and development of conflict of interests of the states in the Syr Darya river basin over an access to water and energy resources in historical perspective: from the Soviet period of water management till the present time; it examines the conflict potential of water-energy resources, both at the regional and at the state level. In order to consider the dynamics of water relations’ development in the Syrdarya river basin the author used a historical-political approach, comparative method, event and causal factor analysis. The article concludes by saying that the water conflicts in Central Asia can be triggered by private interests of separate national entities in each country, rather than hostile inter-state relations.