Disasters such as major floods affect all part of the globe. Hospital and healthcare structures are critical resources during such event and do not always benefit of emergency preparedness. When hospitals are impacted by the disaster, it puts a strain on the system and a reorganisation of all available hospitals on a given territory is necessary. As part of case study applied to the impact of floods on the Île-De-France region's health system, we present in this paper a simulation model that evaluates healthcare emergency plan by combining the healthcare process with the flood dynamics. The results can be used to elaborate an optimized strategy for evacuation and transfer operations. We provide a case study including several medical specialties and quantify the impact of several flood scenarios on the healthcare system. Highlights • Flood dynamics Markov model • Patient flow discrete-event model • Operational flood emergency management planning tool at the territory scale • Evacuation decision tool for hospital manager