This paper develops a systematic assessment of the sustainability of ecosystem services provided by rivers impacted by water storage projects. Given the conflicting preferences amongst stakeholders and the incomplete, uncertain and contradictory understanding about river ecology it is recognized that managing water resources sustainably is a wicked problem. In order to address this wicked problem, the methods of multi-criteria analysis and graph analysis are applied, in accordance with integrated water resource management, to assess the potential of investing in water storage projects and explore for sustainable solutions through the construction of an ecosystem services index.