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This paper addresses the influence of sea level changes on the stratigraphy and basal topography of latest Pleistocene–Holocene incised valley fill of the Arakawa and Menuma Lowlands in central Japan by using sedimentary drill cores and columnar geologic sections. In the study area, four buried fluvial terrace surfaces (I to IV) formed in response to sea-level fall during the last glacial period. Surface III is covered with As-YP tephra (15–16.5 ka) and extends at least 65 km landward from the present mouth of the Arakawa River. A buried valley named surface V that extends from at least 85 km upstream from the present river mouth to about 120 m below present sea level on the continental slope was incised in response to the sea-level lowstand of the Last Glacial Maximum. The incised valley fill can be divided into three units: unit A (gravelly river channel sediments including valley-bottom gravels), unit B (fluvial sediments), and unit C (marine sediments), which intertongues within unit B and pinches out up to 60 km upstream from the present river mouth. Unit C marks the landward limit of Holocene transgression. The lower part of unit B is a fining-upward succession formed during rising sea level and indicates retrogressive aggradation of floodplain sediments during transgression, whereas the upper part of unit B was formed during a sea-level highstand. The floodplain migrated more than 85 km upstream from the modern shoreline in response to sea-level rise until the middle Holocene and extends over several tens of kilometers beyond the landward limit of the Holocene marine transgression.