Flooding events are rising across European watercourses because of changing climatic conditions and anthropogenic pressure. To deal with these events, the European Floods Directive requires the development of flood risk management plans regularly updated every 6 years, where areas affected by flood risk and relative management strategies should be identified. Along the Directive, sediment transport and morphological changes in freshwater environments like rivers are only marginally considered, leading to a possibly wrong estimate of the impact of floods in the case of watercourses in which sediment transport represents a fundamental component. Using the Secchia River in Italy as a case study, the paper compares two numerical simulations performed with the freeware iRIC suite, imposing the same boundary conditions but comparing fixed and mobile bed. The obtained results pinpoint the importance of considering sediment transport in drawing flooding scenarios for alluvial sandy rivers. As suggested by this example, for the incoming revisions of the flood risk management plans, forecasted by 2021, water managers should account for the dynamic behaviour of surface watercourses, considering sediments not only as a driver of pollutants but also as a key aspect that shapes the environment and should be considered in modelling future scenarios and drawing associated management strategies.