Water management has evolved in the last years towards more integrated and participatory approaches, aiming at improving the adaptability of water systems. Following this line, we propose a methodology to build a decision support system, based on the participation of stakeholders and the integration of the different disciplines involved in water use, as well as the inclusion of uncertainties in the management planning. The process has been implemented in the Upper Guadiana basin (Spain) with the aim of solving the existing conflicts: the aquifer, which is the main water source in the area, has been over-exploited during the last decades for irrigation. This has lead to serious degradation of natural water-related ecosystems and important social conflicts. The river basin authority has tried to implement different policies to attain the aquifer recovery, so far without much success. At present, a new management plan specifically for the Upper Guadiana has been approved, where some policy measures are proposed for attaining the reduction of agricultural water consumption. The methodology proposed in this work is based on the combination of a Bayesian network and an economic mathematical programming model, elaborated with the active participation of stakeholders. The resulting DSS will be used to evaluate different management options, within those included in the Special Plan of the Upper Guadiana, in terms of their impacts on the agricultural income and the environmental sustainability. Results show that new measures would not be successful unless they are accompanied by an increase of compliance of farmers with water regulations.