The lower Ebro River experiences long-term hydrological and sedimentary adjustments following major regulation. Alterations in water and sediment fluxes have enhanced a massive macrophyte colonization that, in turn, generates a series of ecological and socio-economic problems. Controlled water releases, so-called flushing flows (FFs), have been designed and implemented since 2002 in this part of the river with the objectives of controlling macrophyte populations and maintaining sediment transport in the channel. FFs may produce adverse geomorphic effects, such as bed incision driven by the increased sediment transport capacity and the lack of sediment replacement from upstream. It is thus important to evaluate the potential geomorphic responses to a specific FF design, and redesign FFs regularly to maximize macrophyte removal while minimizing the undesired consequences. Geomorphic responses associated with FFs can be assessed using hydraulic and sediment transport models. In this paper, we use the hydrodynamic model CCHE2D® to evaluate the role of a monitored FF on a river's geomorphology. The designed FF had a duration of 13 h, attaining a maximum discharge of 1350 m3 s−1. A total of 3375 t of fine material were transported during that event. CCHE2D® model performance is evaluated in terms of hydraulics and sediment transport by comparing observed with modelled values (i.e. discharge, water surface elevation, sediment loads). Overall, objective functions indicate that simulations are in agreement with field observations. For instance, the Root Mean Square Error (RMSE) between the observed and modelled FF hydrograph was 93 m3 s−1, whereas the RMSE of the total load was 71 t. The example modelled here shows that the FF design typically implemented in the lower Ebro does not cause severe geomorphic impacts. The model provides visualization of the spatial patterns of erosion and deposition for the first time, allowing identification of critical zones where degradation or aggradation may occur. Copyright © 2012 John Wiley & Sons, Ltd.