Accurate calculation of secondary flows is critical for the accurate calculation of the sediment transport field in topographically-induced non-uniform flows, and thus the morphodynamic evolution of a river, because the secondary flow can significantly change the direction of the near-bed flow and sediment transport as compared to the vertically-averaged velocity vector. In this study, a non-hydrostatic, free water-surface, three-dimensional, numerical model is developed for flow around a spur dike. The model employs a Body Fitted Coordinate (BFC) system and a moving grid system. These methods enable the model to fit the grid to the boundary during free water surface fluctuations. Turbulence larger than the scale of the grid is modeled by the Large Eddy Simulation (LES) technique. LES integrates the spatially-filtered Navier-Stokes equations, which means that time-fluctuating components of secondary flows are numerically calculated. Model results are compared to those of existing experiments around spur dikes.