This paper provides a dataset to develop a diatom-based transfer function, which is applicable to paleoseismic studies at southwestern Kuril subduction zone, northern Japan. Modern diatom samples were collected from five transects from saltmarshes of Lakes Akkeshi and Onnetoh along the Pacific coast of eastern Hokkaido. The relationships between diatom species and environmental variables were elucidated by canonical correspondence analysis (CCA) and partial CCAs. Partial CCAs associated with Monte Carlo permutation tests show that elevation accounts for a significant portion of the total variance in the diatom data. Therefore, statistically significant transfer functions quantifying the relationship between modern diatom assemblages and elevation were developed using weighted averaging partial least squares and applied to fossil diatom assemblages from Lake Onnetoh. The reconstructed curve of elevations contains five emergence and four submergence events and the transfer functions calculated the amplitude of four of the emergence events to be at least 1 m. The results are consistent with paleoecological data produced by previous studies. If these events represent uplift associated with interplate earthquake and subsidence during an interseismic period along the Kuril subduction zone, transfer functions of eastern Hokkaido can contribute to reconstruction of the recurrence intervals and the amplitude of earthquakes.