The Zayandeh-Rood river basin is the only permanent and water-rich river in the central plateau in a densely populated area with a dry and semi-arid climate. Due to precise historical management and supervision, the social problems of water distribution rarely happened. However, since the mid-1980s, the river has steadily lost its natural flow and has become seasonal river. Therefore, there have been many protests by stakeholder in the provinces. The purpose of this paper is to investigate the reason for the water crisis in the Zayandeh-Rood river basin has occurred over the last two decades. The knowledge of water management is beyond the technical understanding of the subject, and it is an interdisciplinary science, so it should be considered in different fields. Thus, this article focuses on recognizing the water governance gap in the Zayandeh-Rood river basin in various sectors. The method used for this purpose, is analysis of documents, based on a comparative content analysis. Also we conducted interviews with 30 water experts in different districts and provinces (Isfahan, Chaharmahal and Bakhtiari). The results showed that water governance in the Zayandeh-Rood River basin resulted in various gaps, including executive gaps, targeting gaps, policy gaps, information gaps, capacity gaps, investment gaps, and responsibility gaps.