We are developing a numerical model for simulating the development and migration of dunes in rivers in a 3D case. The numerical model consists of three steps: turbulent flow, sediment transport and morphology. We modelled the turbulent flow using state-of-the-art techniques for detailed hydrodynamics. A finite volume method combined with an isotropic unstructured Cartesian grid with local refining is developed for simulating time-dependent incompressible flow. The grid can be refined and adapt to the boundaries. The governing equations are discretized using a staggered grid and advance in time using the fractional step method. The Cartesian grid cells and faces are managed using an unstructured data approach. A ghost-cell immersed-boundary technique has been implemented for the cells which intersect the immersed boundaries. Because of the importance of coherent structures of turbulence on sediment transport, the turbulence regime is modelled by Large Eddy Simulation. The sediment is considered as rigid spheres in the turbulent flow. Models for pickup, transport and deposition are incorporated in the current study. The morphodynamics is determined by the rate of pickup and deposition of the sediment particles.