A nonlinear three-dimensional two-way coupled fluid-sediment interaction model is developed in this study. The model is composed of a generalized Navier–Stokes solver (GNS) with a volume of fluid module for air-water interface tracking and a sediment transport module (STM) for fluid-sediment interface tracking. The GNS model is based on the finite difference method with a turbulent stress model of large-eddy simulation to compute incompressible viscous multiphase flows. The STM is used to compute nonlinear sediment bed profile change due to bed-load sediment transport. A two-way coupling scheme connecting GNS with STM is implemented at each time step to ensure the fluid-sediment interaction. For validation, the fluid-sediment interaction model is applied to predict cross-shore profile change of a sloping beach due to breaking solitary waves, and the resulting predictions are examined and compared with the measured data from a set of hydraulic tests. It is found that the fluid-sediment interaction model predicts reasonably well the sediment transport and the resulting beach profile change. The sensitivity of model parameters involving the sediment transport to the beach profile change is analyzed. Finally, the fluid-sediment interaction model is applied to predict local scour in front of a quay wall due to a jet flow to demonstrate its applicability to general three-dimensional problems.