The indirect impacts of flooding on transportation networks include, among others, consequences of the service disruption for the users. Indirect impacts are of a wider scale and with a longer incidence in time than direct impacts. The key aspect for the quantification of indirect impacts of flooding is the assessment of the disruption of the transportation service, with social and economic consequences. In this work, a traffic model for a pilot zone is constructed for accurate quantification of the functionality of the network after the failure of infrastructure components such as road segments and bridges. A mesoscopic simulation, which is capable of building a road network model, assigning trip paths with the impact of road closures, and evaluating travel time and vehicle volume redistribution in a given disruption scenario, was used to identify the traffic disruption in the face of flood events. Modelling outputs from a case study in the Santarém region of Portugal indicate which roads are more congested in a day. A comparison between the baseline and a flood scenario yields the impacts of that flood on traffic, estimated in terms of additional travel times and travel distances. Therefore, simulating and mapping the congestion can largely facilitate the identification of vulnerable links.