We conducted a geo-slicer survey and taxonomic study of fossil diatoms in the Toberi River mouth area, Hokkaido, Japan, to clarify fossil diatom assemblages during the last millennium as background data for paleoenvironmental studies. We collected sediment samples and identified 185 diatom taxa belonging to 67 genera, though we were not able to identify 30 taxa at the species level. In the study area, two major diatom assemblage changes during the last millennium, were recognized. One occurred after the 19th century and could be attributed to anthropogenic factors, and the other may have been caused by tectonic movements associated with great earthquakes that occurred along the Kuril Trench in the 12–13th and 17th centuries.