In this study, we investigated the relationship between seasonal/annual variation in water masses and nutrients, and the effects of nutrients on phytoplankton assemblages in the western Korea/ Tsushima Strait. We collected water samples at least once per month from March 2006 to January 2008. There was seasonal variation in nutrient concentrations, with higher values in winter than in summer, and there was annual variation in chlorophyll-a concentration and phytoplankton abundance during spring, with values being approximately three and 10 times higher, respectively, in 2007 than in 2006. Phytoplankton abundance was also approximately four times higher in 2007 than in 2006 during the stratification periods. Our findings suggest that when the supply of nutrients to the upper layer is increased as a result of the Tsushima Warm Water Current and the effect of typhoons, they regulate the abundance and composition of phytoplankton assemblages in the Korea/Tsushima Strait, inducing a succession from flagellates to diatoms.