Azerbaijan´ s water challenges and threats, highlights the necessity of paying attention to water management. The present article addresses the following question: what are the serious obstacles for the implementation of water management in the Republic of Azerbaijan? This question is formulated against the backdrop of the following given: water crisis in republic of Azerbaijan is rooted in the shortage of economic water rather than tangible water. The hypothesis is that reemphasis on the role of government, lack of attention to the system of water co-management, lack of integrated management of water resources based on watershed divisions as well as inappropriate water infrastructures are the four main obstacles. In order to compensate the existing shortcomings, the Republic of Azerbaijan has chosen the approach of partnership with international institutions especially European Union, and is less dependent on its own scholars and scientific researches. Using explanatory – analytical research method and documentary methodology, the authors try to tell why the research findings provide an answer to the research question.