The Fuji River flows approximately 128 km from north to south near the center of the Japanese archipelago, with its mouth located near the collision boundary between the Eurasian Plate and the Philippine Sea Plate. To investigate the Holocene activity of an onshore subduction thrust at the northern end of the Nankai Trough, we measured radiocarbon ages of terrestrial plants and marine shells in sediments collected from across the Fuji River. Ten sediment cores, Ng-1 to 4, Km-1 to 5, and Nz-1, were obtained from an uplifted terrace to a subsidence lowland along the border of Suruga Bay. Based on analyses of lithology, molluscan assemblages, and radiocarbon dating, the cores were classified into six sedimentary facies. In ascending order, they are river channel, floodplain, estuary, estuary front, inner bay, and lagoon. These paleoenvironmental changes are primarily associated with sea-level fluctuations and tectonic movements during the post-deglacial period. The terrestrial accumulation curve aligns with the horizons of Kawago-daira pumice and Kikai-Akahoya volcanic ash. Reservoir ages of six pairs from the estuary to inner bay facies of the Ng1 core ranged from 150 ± 70 to 470 ± 60, during the period from 7900 to 6800 cal BP, and their average was calculated to be 310 ± 120 years. The chronological changes in the reservoir effect can be correlated with Holocene sediments from the coastal area of Southwest Japan under the influence of the Kuroshio warm current.