Abstract: The article considers some issues of modern processes of regionalization in Central Asia as a possibility of regional self-identification in the new context. Different starting economic development potential of the newly independent States has determined the strategy of inter-state relations. Special attention is paid to the analysis of the political situation in the region after the collapse of the USSR in the context of the disputed territories and joint water use of transboundary rivers.Unfair, from the point of view of the Central Asian countries, division of state borders, conducted in Soviet times, still hampers building up a full-fledged cooperation with the neighbors in the region. Border conflicts often end in armed clashes. Water and energy resources are also an important factor in the Central Asian interaction, which leads to an open confrontation between the upstream and the downstream countries on the issues of hydropower potential use.In the article factor analysis and interdisciplinary approach to the study of the intra-regional conflicts of transboundary water resource use is applied. Different attempts of interstate collaboration and causes hampering this process are considered. The negative role of border, energy and water conflicts in regional cooperation is reflected in the article. The study of transformation processes in Central Asia makes it possible to state that the political and economic development of the countries is uneven, inconsistent, and is formed on the basis of objective and subjective factors. The low degree of intra-regional cooperation beyond integration associations leads to economic and political dependence of each country on the influential global actors.