A sediment transport calculation was proposed, which consistently considered the influence of laminar and turbulent resistance forces caused by infiltration/exfiltration. From a comparison of the nondimensional bed–load sediment transport rate, it was found to be essential to consider both laminar and turbulent resistance forces when formulating the influence of infiltration/exfiltration in sediment transport calculations. A three-dimensional coupled fluid–structure–sediment interaction model was improved using the proposed sediment transport calculation, and applied to tsunami-induced local scouring around an inland structure. Numerical results showed that consideration of infiltration/exfiltration improved the computational accuracy of the prediction of a scour hole formed around the seaward edge of the structure, and accordingly the improved model could capture the evolution of the scour hole with sufficient accuracy. This suggests that the improved model should be a useful tool for assessing tsunami-induced local scouring.