Large eddy simulation was used to investigate the spatial development of open channel flow over a series of dunes.The three-dimensional filtered Navier-Stokes (N-S) equations were numerically solved with the fractional-step method in sigma coordinates.The subgrid-scale turbulent stress was modeled with a dynamic coherent eddy viscosity model proposed by the authors.The computed velocity profiles are in good agreement with the available experimental results.The mean velocity and the turbulent Reynolds stress affected by a series of dune-shaped structures were compared and analyzed.The variation of turbulence statistics along the flow direction affected by the wavy bottom roughness has been studied.The turbulent boundary layer in a complex geographic environment can be simulated well with the proposed large eddy simulation (LES) model.