Southwestern Hokkaido faces intricate physiological and chemical changes. Subsequently, changes in lower trophic levels are of concern, but fully understanding the relationship between microplankton and hydrography in this region is required. To examine the relationship between the microplankton community (diatoms, dinoflagellates, ciliates, and euglenoids) and environmental factors in Suttsu, Hokkaido, water samples were collected at 4–15-day intervals from August 2020 to August 2022 at Yokoma Port. Diatoms were dominant in the study area, with an apparent seasonal change in species composition. Lower phytoplankton cell density was observed in the second year than in the first year during autumn and winter because of low temperatures and light intensity in the second year. A significant decrease in the number of attached diatoms (Navicula spp.) was observed during the winter of the second year, possibly due to calm conditions (low tide and wind speed), which prevent the detachment of weakly attached species. Large blooms of euglenoids (Eutreptiella gymnastica and E. marina) in April and May were caused by the exclusive use of nutrients from the inflow of river water during the snowmelt season. Warm-water species sporadically occurred, suggesting their transportation by the Tsushima Warm Current. Temperature, nutrients, and light intensity primarily control microplankton communities, which vary seasonally. These findings led to the prediction of lower trophic levels due to the impact of warm water inflow.
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