Basin-wide approach in managing water resources is believed to be the most effective way in addressing upstream and downstream flows. However, this poses certain challenges as water basins tend to be transboundary and include a plethora of stakeholders and their interests. In order to avoid conflictive and rival behavior riparian parties engage in agreements and institutional collaborations in a form of river basin organizations (RBOs). Hence, it is crucial for these institutions to effectively respond to emerging challenges and keep the parties cooperating. In the current study I conducted a desk-study assessment of an RBO answering the research question: How assessment of effectiveness of RBOs can affect their institutional arrangements? In order to answer this question, I assessed dependent variables of operational effectiveness of an RBO and connected this analysis with the existing institutional arrangement. Further, obtained results were used as the basis to provide recommendations for further improving of the resistance of an RBO to external processes. As the case study, the International Fund for Saving the Aral Sea (IFAS) was proposed, which is an existing RBO established by the five Central Asian riparian states in 1993 to manage the water allocations of two transboundary rivers and preserve the Aral Sea. Analysis of its effectiveness of a period 1993-2016 delivered a broader set of recommendations both for IFAS and for the chosen theoretical framework.