Sediment bypass is an excellent reservoir sedimentation countermeasure which can achieve both reduction of sediment flowing into the reservoir and supply of sediment to the downstream of the dam. Sediment bypass facility has been almost completed at the Koshibu Dam in the Tenryu river, and test operation is scheduled from 2016. In order to optimize the bypass operation, further study is needed in sediment transport at the diversion facility. Then, full three-dimensional calculation depending on the operation of sediment bypass facility was performed using the improved model that can calculate the bed deformation and complex flow around the diversion facilities. Based on this calculation, time depending changes in bypassing volume of sediment, and the sediment bypassing ratio based on the river bed level was investigated. Finally, the process of inflow, deposition and discharge of sediment in the bypass facility was described, and the effective conditions that can increase the bypassing ratio was proposed.