This paper proposes a novel methodology for modelling the impacts of floods on traffic. Often, flooding is a complex combination of various causes (coastal, fluvial and pluvial). Further, transportation systems are very sensitive to external disturbances. The interactions between these two complex and dynamic systems have not been studied in detail so far. To address this issue, this paper proposes a methodology for a dynamic integration of a flood model (MIKE FLOOD) and a microscopic traffic simulation model (SUMO). The flood modelling results indicate which roads are inundated for a period of time. The traffic on these links will be halted or delayed according to the flood characteristics—extent, propagation and depth. As a consequence, some of the trips need to be cancelled; some need to be rerouted to unfavourable routes; and some are indirectly affected. A comparison between the baseline and a flood scenario yields the impacts of that flood on traffic, estimated in terms of lost business hours, additional fuel consumption and additional CO2 emissions. The proposed methodology will be further developed as a workable tool to evaluate the flooding impact on transportation network at city scale automatically.