Seismic wave amplifications were investigated using strong-motion data obtained from the ground's surface (K-net) on the Kii peninsula (southwestern Japan) and from the network of twenty seismic stations on the seafloor (DONET) located off the peninsula near the Nankai trough. Observed seismograms show that seismic signals at DONET stations are significantly larger than those at K-net stations, independent of epicentral distances. In order to investigate the cause of such amplifications, seismic wavefields for local events were simulated using the finitedifference method, in which a realistic 3D velocity structure in and around the peninsula was incorporated. Our simulation results demonstrate that seismic waves are significantly amplified at DONET stations in relation to the presence of underlying low-velocity sediment layers with a total thickness of up to 10 km. Our simulations also show considerable variations in the degree of amplification among DONET stations, which is attributed to differences in the thickness of the sediment layers. The degree of amplification is relatively low at stations above thin sediment layers near the trough axis, but seismic signals are much more amplified at stations closer to the Kii peninsula, where sediment layers are thicker than those at the trough axis. Simulation results are consistent with observations. This study, based on seafloor observations and simulations, indicates that because seismic signals are amplified due to the ocean-specific structures, the magnitude of earthquakes would be overestimated if procedures applied to data observed at land stations are used without corrections.