Unprecedented large-scale algal blooms were observed during autumn 2021 around the Katsurakoi fishing port, Kushiro, eastern Hokkaido, Japan. Monitoring of shoreline water showed that chlorophyll a (Chl a) concentrations and the cell density of Karenia spp., dominated by Karenia selliformis, repeatedly increased synchronously between September and November 2021. These increases were associated with a southerly wind-driven current, which transported offshore water on the shelf towards the shoreline at the sea surface. The blooms were prolonged as a result of algal accumulation in the semi-closed fishing port. The maximum Chl a concentration and cell density exceeded 50 µg Chl a/L and 10⁴ cells/mL, respectively. During the autumn bloom of Karenia spp., the nitrate?+?nitrite and phosphate concentrations in the water were lower than those in 2019 and 2020, and the silicate concentration was comparable. The ammonium concentration during the bloom was notably higher than before the bloom period, reaching 15 µM. Mass mortality of several fish species and echinoderms that were cultured using rearing water intake from the same shoreline occurred synchronously with the increase in Karenia spp.