Economic development as one of the important indicators of the development is based on the optimal allocation of resources. In the past, capital, human and natural resources were the major sources of development. Considering the role of technology progress era to achieving development goals, implies also the importance of knowledge as one main sources of development. On the other hand, water scarcity is one of the main challenges in MENA countries, and especially in Iran, which doubles the importance of achieving water, food and energy security. The aim of this study is to identify the problems of water research network and indicate the factors that increase the effectiveness of the water research system in Isfahan. In other words, the focus of this research is to analysis the context of collaboration. The methodology of this study was the qualitative research approach and the grounded theory method. Data collection was based on in-depth key informant interview by open and semi-structured questionnaires. The results showed that the main problems of water research system are: disbelief and no need to research outcome, fragmented and centralized policy making, the dominance of paper publishing in the regulation of faculty promotion, no research strategies and leadership, lack of holistic approach and inter (trans)-disciplinary research in problem solving and being only involved in the organization’s routines. Keywords : Qualitative research, Grounded theory method, Regulation of faculty promotion, Belief in research outcome, Research strategies and leadership, Inter (Trans)-disciplinary research.