The flow and the scour around a coastal structure due to tsunami flows are simulated by combination of the Large Eddy Simulation method of calculating turbulent free-surface flows and the bed-load sediment transport calculation method. The tsunami wave impinging on a structure is the case for which experimental data are available and the simulation results are compared with. Then the tsunami overtopping a seawall and the scour of its foundation, as seen at several sites during the East Japan Earthquake of 2011 is simulated. The wave impingement calculation is reproduced well and the scour simulation is reasonable compared with exsisting estimates. For more realistic simulation of long-period or equilibrium scour hole estimation, transport of the suspended sediment will be needed.