To help characterise the palaeogeographic and lacustrine environmental changes that resulted from the Holocene transgression and residual subsidence in the eastern Kanto Plain of central Japan, we analysed four drill cores and reviewed other core data from the southern part of the Lake Inba area. Fossil diatom assemblages yielded evidence of centennial-scale palaeogeographic and salinity responses to sea-level changes since the late Pleistocene. We determined that the seawater incursion into the Lake Inba area during the Holocene transgression occurred at approximately 9000 yr. We also recognised a late Holocene regression event corresponding to the Yayoi regression, considered to have occurred from ca. 3000 to ca. 2000 yr, and a subsequent transgression. Our data clarify some of the palaeogeographic changes that occurred in the Lake Inba area and document an overall trend toward lower salinity in the lake during the regression. In particular, the environment in Lake Inba changed from brackish to freshwater no later than 1000 yr. From the detailed palaeogeographic and palaeo-sea-level reconstruction, we recognised that residual subsidence occurred during the Holocene in this area. Thus, comparison of sea-level reconstructions based on modelling and fossil diatom assemblages is effective in interpreting Holocene long-term subsidence.