In this study, we performed a riverbed variation calculation for the Harukigawa River, where the grain size of the produced sediment was coarse, to reproduce the riverbed variation and sediment discharge caused by typhoon events during 2011 and 2012. We used a riverbed variation calculation model that considers the phase shift of fine sediments during sediment transport. The condition for the phase shift of fine sediment is given by u＊αPSω０, as proposed by Uchida et al. (2018). In the reproduction calculations, multiple calculations were performed with varying values of αPS. The reproducibility of the calculation results was verified against the measured values of riverbed fluctuation height and passing sediment volume. The results showed high reproducibility under conditions of αPS= 2 to 4, as confirmed by the flume experiment conducted by Hina et al. (2018). When the phase‐shifted sediment particle size distribution was examined in this calculation, it was found that the spatio‐temporal change in phase‐shifted particle size was small during the time period in which the phase shift occurred. The high reproducibility of the model that accounts for phase shift is attributed to the small amount of phase‐shifted sediment, and the resulting minimal increase in pore fluid density. Additionally, when the phase shift was considered, the sediment flow capacity of the sediment‐moving layer increased and the amount of sediment deposited on the river bed decreased. Consequently, the riverbed became coarse‐grained, less sediment floated, and the suspended load in the water layer decreased. As a result, a trade‐off occurred between the sediment in the moving sediment layer and the suspended load in the water flow layer, which made it difficult for the total amount of sediment to change. These results show that the phase shift evaluation method adopted in this study is applicable to a wide range of gradient and grain size conditions.