Recently, coastal disasters due to long-period swells induced by heavy storms and catastrophic typhoons have increased at Japanese coasts and harbors. Long-period swells are more susceptible to the bottom bathymetry of the offshore deep water region and their wave heights locally increase due to the concentration of wave energy caused by the complex bottom bathymetry in the relatively shallow water region. In addition, the wave overtopping rate may increase due to the long waves in front of the seawall induced by the long-period swells. However, the spatial relationship between wave characteristics and wave overtopping discharges in the complex bathymetry are not well known owing to a lack of detailed measurements. In this study, model experiments were conducted by using a large basin to investigate the spatial characteristics of wave transformation and wave overtopping focusing on the heavy wave overtopping damages caused by the arrivals of long-period swells at the Shimoniikawa Coast in 2008. Effective countermeasures against wave overtopping are also discussed based on their characteristics.