This paper describes the multi-agent organization of a computer system that was designed to assist operators in decision making in the presence of emergencies. The application was developed for the case of emergencies caused by river floods. It operates on real-time receiving data recorded by sensors (rainfall, water levels, flows, etc.) and applies multi-agent techniques to interpret the data, predict the future behavior and recommend control actions. The system includes an advanced knowledge based architecture with multiple symbolic representation with uncertainty models (bayesian networks). This system has been applied and validated at two particular sites in Spain (the Jucar basin and the South basin).