Magnitude 8 megathrust earthquakes that have generated large tsunamis with wave heights of >5 m in coastal areas of southwestern Japan have occurred every 100–150 years along the Nankai–Suruga Trough, which marks the convergent boundary between the Eurasian and Philippine Sea plates. Using sedimentological, geochemical, and paleontological analyses, as well as 14C dating, we examined tsunami deposits in 12 sediment cores collected from the Hamatome lowland, Yaizu Plain, Shizuoka, which faces the Suruga Trough. Four sandy tsunami deposits (Sands 1–4) are identified in sediments deposited during the last 5000 years. Sand 1 was deposited between 805 and 405 BC, suggesting that only one tsunami left a sedimentological imprint in the Hamatome lowland lagoon during the period of ∼4000 years between 3090 and 2913 BC and the AD 1096 Eicho-Tokai earthquake. This very low frequency of tsunami inundation may suggest that this tsunami was larger than those typically associated with megathrust earthquakes. Sands 2–4 are correlated with tsunamis associated with the Eicho-Tokai, AD 1361 Shohei-Koan, and AD 1498 Meio-Tokai earthquakes, respectively. Our data indicate that a sand spit, which had previously protected the lagoon from oceanic waves, was abruptly destroyed following the AD 1096 Eicho-Tokai earthquake and did not re-form at the same location. This disappearance of the sand spit is inferred to have involved an earthquake-induced submarine landslide. The data presented in this paper, together with information obtained from historical documents, indicates that M8 megathrust earthquakes in AD 1096 and AD 1498 caused submarine landslides in the study area, resulting in coastal subsidence and damage to coastal areas additional to that caused by the tsunamis.