Hakodate Bay at the southern end of Hokkaido experiences physical and chemical environmental changes in the adjacent Tsugaru Strait. Harmful algal blooms have occurred since 2015. However, information on the relationship between environmental variables and the entire protist community or the mechanisms causing harmful blooms in the Hakodate Bay is lacking. We investigated the seasonal changes in the protist community using weekly field sampling to reveal the relationship between the protist community and environmental variables in the Hakodate Bay. Based on cluster analysis, six groups were identified: Winter, Spring, Late Spring, Summer, Benthic, and Karenia. From the Winter to Spring group, a species transition from low-temperature-adapting Thalassiosira spp. to Chaetoceros spp. was found, which is well described in the subarctic regions. The Summer group comprised high-salinity-tolerant species (the diatom Leptocylindrus danicus and dinoflagellate Prorocentrum spp.) because of high fluctuations in salinity due to precipitation. The other groups (Late Spring, Benthic, and Karenia) randomly filled the spaces between the three groups. The dinoflagellate Scrippsiella spp. was dominant in the Late Spring group because of accumulation by wind-driven currents. Because a strong relationship between benthic species and wind speed was exhibited, the Benthic group comprised benthic diatoms released into the water by mixing. The Karenia group was observed only from late August 2021 to early January 2022, when higher ammonium and lower light conditions (i.e., cloudy conditions) were detected than during the same period in the previous year. Owing to environmental conditions, diatom growth was restricted by low light intensity, whereas that of Karenia mikimotoi increased by taking advantage of the abundant nutrients. Seasonal changes in the protist community of the Hakodate Bay can generally be explained by temperature and nutrients; however, in the short term (1–2 weeks), changes were also influenced by meteorological conditions (solar radiation, wind, and precipitation).