Fluvial channels present bed forms such as dunes and ripples that alter instantaneous hydrodynamics parameters such as flow velocities, water surface profiles, bed shear stresses, and Reynolds stresses and create turbulent coherent structures that are significantly different from those presented in flat bed conditions. It is known that LES-based models are more suitable than RANS models to reproduce the complex hydrodynamics around bed forms. Herein, a LES model is applied to describe the mean and turbulent flow structure under superimposed bed forms. Three cases were simulated: RUN I (train of ripples), RUN II (superimposed bed forms), and RUN III (amalgamated bed forms). The LES modeling was performed using a free surface condition to allow the model to develop undulations and boils on the water surface caused by effect of the bed forms. Some important conclusions from this study are: the division of high and low shear stresses on the stoss side of the dune, the progression of the flow field topology from RUN I and RUN III, and the type of turbulent coherent structures found in each stage. The region of high shear stresses was related to turbulence production, in which the streamwise velocity fluctuations (where strips structures are related to streaks) were associated to the modification of the bed morphology. The turbulence Horseshoes Vortices (THV) were more frequent in RUN I than in the other two cases (where streamwise rolls were more frequent). Finally, the frequency of the bursting events increased from RUN I to RUN II and decreased from RUN II to RUN III. Implications of detailed hydrodynamics into bed forms processes are also presented and discussed.