Flash-flood events in mountain basins often involve large volumes of sediment transported by the rivers, with significant changes in the bed morphology even within a single, short-term event. By contrast, flood scenarios are most frequently devised under the assumption of a fixed-bed condition, that is, neglecting the possible change of the river bed elevation during the reference flood. In this work, feasibility and positive outcome of incorporating sediment transport modelling into the evaluation of flood hazard are assessed with reference to the case of the Mallero River in northern Italy. A past flood event has been modelled by means of a fully coupled model of flow and sediment transport. Particular attention has been focused onto the town of Sondrio, located at the downstream end of the river. Results show that interpretation of the event dynamics and proper quantification of flood hazard for the town cannot be obtained without considering the morphologic evolution of the river bed due to sediment transport. In addition, reliability of the results of hydro-morphologic modelling has been proved by extensive sensitivity analysis, showing a weak dependence of the findings on external forcing. Some arguments are thus provided towards the incorporation of morphologic processes into hazard assessment, landscape protection, scenario modelling and emergency management.