This study discusses the mechanism for the occurrence of equilibrium and non-equilibrium scour holes. By using a particle image velocimetry (PIV) measurement system, it measures the turbulent flow fields in an open channel moving through the rough bed below a groundsill. Then, the Reynolds-stress model (RSM), embedded in FLUENT software, is applied to perform a numerical simulation. The experimental results show that at equilibrium, the location of the re-attachment point is significantly affected by the flow discharge. Further, the re-attachment point of the scour hole affects the size and range of the counterflow zone, which becomes the main region for deposits in the natural channel. In addition, the formation of erosion is mainly affected by turbulence intensity and Reynolds stress. However, in non-equilibrium scour holes, our results clearly show that the turbulence intensity and the Reynolds stress are significantly larger at the end of the scour holes near the bed due to the continual development of the scouring. The correlation between the numerical simulation and experimental results are also examined. Overall, it can be seen that the simulated mean velocity profiles are quite consistent with the measured data. However, in terms of turbulence intensities and Reynolds stress, the simulated results could be overestimated when compared with the measured data; they are overestimated with a sudden decrease near the liquid surface. Although, the simulations in the near bed area show some divergence and the trend in the scour hole is quite consistent. Therefore, numerical simulations can be performed in advance to act as an important reference when evaluating the safety of downstream structures.