With the collapse of the Soviet Union, the centralized and highly complex mechanism for water resourced allocation in Central Asia turned into a complex cross-border water management problem and left unresolved bilateral claims. Under such a situation, transboundary rivers caused national and regional instability and created a new source of conflict between coastal governments by abandoning regional integration in Central Asia. In addition to natural and historical reasons, the tie between water and energy issues, climate change, population growth and its disparate distribution in Central Asia has exacerbated the security challenges of the water issues in the region. Accordingly, the main question of the present paper is that "On what principles the management of transboundary rivers in Central Asia has been based since the Republic’ s independence and how it has affected the security of this region? " The findings of the research, which are descriptive-analytical using documentary and transactional methodology, show that "the principles ruling management of transboundary rivers in Central Asia during the past quarter century have been based on competition, self-orientation and separate national interests of the Republics in Central Asia which have led to local and national conflicts and can be studied as an indirect or complementary source of security instability in Central Asia. ”