Diatom composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido, Japan, showed significant spatial variation in abundance and taxa within a spatial extent of 10–15 km. Environmental variables such as temperature, salinity and nutrient contents, and geographical feature of the coast were related to our observed variation. The variation in the environmental factors appear to be strongly affected by both the Coastal Oyashio Water and terrestrial input by Biwase River and surrounding Kiritappu Wetland. Geographical influences are related to the historical connectivity of pelagic waters that are now divided by the peninsula laying between Biwase and Hamanaka Bays. Although this study is based on just a snapshot of data, it is the first dataset collected for Hamanaka coastal water. The obtained data can be used as baseline data for future research, including the evaluation of impacts of ongoing climate change on coastal ecosystems, which is expected to heavily affect the coastal ecosystems and biodiversity of this region.