We reconstructed recurrent coseismic subsidence during the middle Holocene from analyses of sedimentary facies and fossil diatom assemblages in a small drowned valley, the Shinjo lowland, bordering Lake Hamana, near the Nankai–Suruga trough, central Japan. The Lake Hamana region is known for coseismic subsidence during the 1707 Hoei (M8.6) and 1854 Ansei-Tokai (M8.4) earthquakes along the Nankai–Suruga trough subduction zone.A coring survey revealed three widely distributed peat layers in the lowland, with a mud layer overlying each of the two lower peats with a sharp contact. We traced the alternating peat–mud beds for over 300 m along the long axis of a valley. The fossil diatom assemblage analysis revealed that the peat layers were deposited in a freshwater pond/marsh environment, which changed abruptly to an estuarine to inner bay environment, recorded by the mud layers. From the sudden environmental change at the two peat–mud contacts and our radiocarbon dating results, we inferred that coseismic subsidence followed by an invasion of seawater into the lowland occurred at least twice, during a great earthquake that occurred between 5645 and 6635 cal yr BP and during another great earthquake at ca. 5700 cal yr BP.Within the mud layers, the dominant diatom species changed gradually upward from Nitzschia frustulum and Cocconeis scutellum in the lower part to Cyclotella striata and Achnanthes submarina in the upper part. These changes suggest that water depth and salinity gradually increased after the coseismic subsidence. A possible cause of this gradual subsidence is postseismic subsidence following great Nankai-Suruga trough earthquakes.