The bed change analysis near the opening gate of a dam or weir to release deposited sediments have been conducted mostly using the numerical models. However, the use of unverified input parameters in the numerical model is able to produce the different results with natural and real conditions. Also, the bed changes near the opening gate of a dam or weir calculated with a numerical model could be varied depending on the geometry extent included the downstream area with supercritical flow in the model. In addition, the different time steps could provide different results in the bed change calculation, even though other conditions such as input parameters, geometries, and total simulation time were same. Therefore, in this study, hydraulic experiments were performed to validate the eddy viscosity coefficient which is the one of important input parameters in the RMA2 model and relevant to variation of simulation results. The bed changes were calculated using the SED2D model based on flow results calculated in the RMA2 model with the verified and selected eddy viscosity coefficient and also compared with experimental results. The bed changes near the opening gate were underestimated in the numerical model comparing with experimental results except only the numerical case without the modeling section of sediment release pipe and downstream area where the supercritical flow was produced. For the simulation of minimum time steps, different shapes of scour hole were produced in numerical and physical modeling.