Managing water resources in an equitable and sustainable manner in the context of climate change can be arduous in the Mekong region, especially in times of water scarcity. Governments often lack systematic ways to involve local communities and other stakeholders, like academia or the private sector in decision making. As part of the third phase of the Sustainable Mekong Research Network (SUMERNET 2014-2018), a regional assessment was undertaken to support water scarcity management. Two main advisory bodies were created: an expert group, comprising of different stakeholders to provide scientific advice, and a policy group involved with planning processes. Different scenarios were analyzed through the lens of a robust decision support (RDS) framework. The RDS system can help policymakers and key stakeholders determine the durability and sustainability of policy options related to drought and water scarcity management and improve management under uncertainties, such as floods and droughts due to climate change.