We propose a rigorous modeling and methodological effort that integrates statistical implementation of hydrology models in predicting inland and coastal flood scenarios due to hurricanes and a scenario-based stochastic integer programming model which suggests resource and staging area decisions in the first stage and the evacuation decisions in the second stage. This novel study combines physics-based flood prediction models and stochastic optimization for large-scale multi-facility coordination of hospital and nursing home evacuations before impending hurricanes. The optimization model considers scenario-dependent evacuation demand, transport vehicles with varying capacities, and both critical and non-critical patients. Utilizing Hurricane Harvey of 2017 as a case study and actual healthcare facility locations in southeast Texas, we explore various evacuation policies, demonstrating the impact of routing strategies, staging area decisions, flood thresholds, and receiving facility capacities on evacuation outcomes. One of the findings is that choosing staging area(s) and deploying evacuation vehicles optimally considering the uncertainty of the hurricane’s path at the time of decision making could have significant effect on the total cost of the operation and evacuation time experienced by the evacuees. We also show the non-negligible value of the scenario-based staging and routing solution conservatively calculated in relation to a single scenario solution using the concept of value of stochastic solution.