Controlled floods are often used in rivers to remove fine sediments that accumulate within gravel particles. Three-dimensional numerical models can predict the flow field and bed shear stress in a very detailed way. In the present study is to use a three-dimensional model is used to predict flow field, assess the effect of inlet conditions, predict bed shear stress, and bed load transport rates during a controlled flood in a natural river. The study site is the Escoumins River (Quebec), where a dam upstream of the studied reach has been used to create control floods. Field measurements (flow and bed load transport) and 2-D simulation results were available, allowing a comparison between the 3-D model, 2-D model and the field measurements. A body-fitted coordinate grid was used and several inlet flow conditions were tested.