The flow field near a spur dike such as down flow and horseshoe vortex system (HVS) are susceptible to the topographic changes in the local scouring process, resulting in variation of the sediment transport with time. In this study, large eddy simulations with fixed-bed at different scouring stages were conducted to investigate the changes in flow field. The results imply that the bed deformation leads to an increase in flow rate per unit area, which represent the capability of sediment transportation by water, in the scour hole. Moreover, the intensity of turbulent kinetic energy and bimodal motion near the sand bed induced by the HVS were also varied. However, the peak moments between the two sediment transport mechanisms were different. Hence, understanding the complex feedback mechanism between topography and flow field is essential for the local scour problem.