S-net is a large-scale ocean bottom (OB) network in the Japan Trench area, consisting of inline-type 150 observatories equipped with seismometers and pressure gauges. Among them, 41 observatories have been buried about one meter beneath the seafloors in the shallow water regions (water depth <1500 m). We analyzed the strong-motion data recorded at the S-net sites from earthquakes with magnitudes 3.5 < Mw ≤ 7 and focal depths < 70 km to understand the site amplification effect on the recorded motions. We used the spectral inversion technique and obtained some fundamental properties of the earthquake source spectra, path attenuation, and site factors from the horizontal-component S-wave portions of the recordings. We obtained that the source spectra followed the {omega }^{-2} source model generally well, and the estimated magnitudes were mostly within ± 0.3 magnitude units of the catalog magnitudes. The stress drops increased systematically with the focal depths, and the values for the shallow earthquakes in the Pacific Plate were higher than those for the interplate earthquakes with comparable focal depths. The path-averaged quality factors were generally frequency-dependent and were somewhat larger than those in the past studies. The peak site frequencies ranged between about 0.2 and 10 Hz, while the peak amplification factors ranged between 10 and 50. Even though the peak frequencies and amplification factors differed from site to site, the peak frequencies were mostly higher than 2 Hz at the outer trench stations, while they were lower than 2 Hz at many inner trench stations. The amplification factors at a few OB sites in the shallow water regions were comparable with the theoretical ones computed from the 1-D subsea model. The amplification factors at intermediate frequencies (~ 0.3 to 2 Hz) generally increased with P-wave travel time in the sediments estimated from the multi-channel seismic survey. At about 20% of the sites (mainly at the unburied stations), spurious site spectra were recognized at frequencies higher than about 4 Hz. If the site spectra between 4 and 10 Hz are required, using only the X-component records is recommended.Graphical