Estuarine material circulation depends on the presence of both phytoplankton and suspended microphytobenthos in the water column. However, the spatial distribution of suspended microphytobenthos and phytoplankton in estuaries is poorly understood. In this study, the abundance of suspended microphytobenthos and phytoplankton in the water column was determined along the salinity gradient in Lake Furen, Japan, from April to October 2015. Throughout the study period, surface and bottom salinity changed horizontally from <10 to >30. Phytoplankton was the main contributor to spatial increases in total cell abundance in mesohaline water as a result of the lake s hydrographic characteristics and water quality. The suspended microphytobenthos cell abundance in the surface and bottom water decreased with increasing salinity and was affected by the depth gradient. Suspended microphytobenthos cell abundances increased with depth (∼10 and 20% of total cell abundance in the surface and bottom water, respectively), which indicated that they were derived from microphytobenthos on the seafloor. The dominant suspended microphytobenthos taxa (Cocconeis spp. and Melosira varians) were mainly distributed in oligo-and mesohaline water, with peaks in mesohaline bottom water. In contrast, the dominant phytoplankton taxa (Skeletonema spp., Heterocapsa triquetra, and Prorocentrum spp.) were abundant at different salinity levels. The spatial distribution of dominant benthic and planktonic species in the water column was influenced by their tolerance to salinity. Our results suggest that suspended microphytobenthos contribute to microalgal communities in estuaries, especially those in bottom waters. Quantification of phytoplankton and suspended microphytobenthos will allow a better understanding of the effects of their spatial distribution on estuarine material circulation.