Current water governance systems in Central Asian countries are shaped by recent water sector reforms and are past dependent. Since collapse of soviet system, countries of the region are implementing water policies, in line with their national development strategies. Moreover, agricultural reforms, socio-political changes have result new situation in rural areas which are having strong influence on everyday water management. The water management became a playground for different interest groups at all hierarchical levels. In this research, author has been applying institutional analysis, comparative study approach to understand system of water governance in different Central Asian countries. Author tried to link impact of the changes at local, national and regional levels on regional cooperation.