This study aims to examine the spatial variation of diatom abundance and composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido. Terrestrial input via Kiritappu Wetland is expected to affect variation and composition differently depending on the position of the two bays. We conducted an oceanographic survey in June 2014 to measure seawater temperature, salinity, colored dissolved organic matter (CDOM) absorption, nutrient concentrations, and total and size-fractionated chlorophyll (Chl) a concentration at 11 stations of the shallowest (<5 m) parts of the bays. These were grouped into four areas (Areas 1 and 2 in Biwase Bay, and Areas 3 and 4 in Hamanaka Bay) based on the distance of the location from the wetland outlet (nearest in Area 1 to the farthest in Area 4). Diatoms are the major primary producers in the water column. Therefore, we also determined genus level cell abundance and diversity of diatoms to compare similarity among areas. Sea surface temperature was the lowest at Area 4, whereas sea surface salinity was the lowest at Area 1. The contribution of CDOM absorption, an indicator of wetland-influenced river discharge, and silica concentration was highest at Area 1. Total amount of nitrite and nitrate concentrations was the highest at Area 4. Total amount of Chl a concentration was also lowest in Area 1. Our size-fractionated Chl a results revealed that while the size composition of phytoplankton varied among areas, micro-sized (>10 µm) phytoplankton were predominant in Area 4. Finally, diatom composition at the genus level differed greatly among areas. Pennate diatoms were predominant in Areas 1 and 2, but centric diatoms dominated in Areas 3 and 4. Our results suggested great spatial variability in oceanographic conditions among areas, with less influence of wetland and more influence of Coastal Oyashio Water based on distance from the wetland outlet. Diatom composition showed geographical division between Biwase and Hamanaka Bays.