A large-eddy simulation (LES) model has been developed to investigate nonlinear wave run-up and overtopping. The Navier-Stokes equations are solved by using a finite differential algorithm, and the modified Marker-Density Function (MDF) technique (Miyata and Park, 1995) is employed for solving nonlinear free-surface motions. In order to evaluate the present model, three numerical simulations are presented: solitary wave run-up on a vertical wall, flow over a broad-crested weir, and regular waves overtopping a sloping seawall. The results are compared with data from experiments and other numerical models.