A methodological proposal aimed at improving the effectiveness of interactions between the scientific community and local actors for decision-making processes in water management was developed and tested to two case studies, in Europe and Asia: the Upper Danube (Danube) and Upper Brahmaputra (Brahmaputra) River Basins. The general objectives of the case studies were about identifying and exploring the potential of adaptation strategies to cope with flood risk in mountain areas. The proposal consists of a sequence of steps including participatory local workshops and the use of a decision support systems (DSS) tool. Workshops allowed for the identification of four categories of possible responses and a set of nine evaluation criteria, three for each of the three pillars of sustainable development: economy, society and the environment. They also led to the ranking of the broad categories of response strategies, according to the expectations and preferences of the workshop participants, with the aim of orienting and targeting further activities by the research consortium. The DSS tool was used to facilitate transparent and robust management of the information, the implementation of multi criteria decision analysis and the communication of the outputs. The outcomes of the implementation of the proposed methods and DSS tool are discussed to assess the potential to support decision-making processes in the field of climate change adaptation (CCA) and integrated water resources management (IWRM).