The seasonal dynamics of phytoplankton communities in Korean coastal waters (KCWs) are influenced by complex interactions between ocean currents and nearshore human activities. Despite these influences, the understanding of seasonal phytoplankton changes and their environmental relationships in KCWs remains limited. We investigate the influence of the distinct characteristics of the three seas surrounding the KCWs (the Yellow Sea, the South Sea, and the East Sea) on seasonal phytoplankton communities based on field surveys conducted at 23 stations between 2020 and 2021. The East Sea exhibited higher winter temperatures due to the Jeju and Tsushima warm currents, while summer temperatures were lower compared to the other regions, highlighting the role of currents and deeper oceanic waters. The Yellow Sea showed significant freshwater influence with low salinity levels from major rivers, contrasting with the higher salinity in the East Sea. These differences led to a disparity in the productivity of the two regions: the highest value of Chl. a was observed to be 6.05 µg L–1 in the Yellow Sea in summer. Diatoms dominated in nutrient-rich conditions, particularly in the Yellow Sea, where they comprised up to 80–100% of the phytoplankton community in summer, winter, and spring. PCA analysis revealed positive correlations between diatoms and Chl. a, while cryptophytes, which thrive in the absence of diatom proliferation, showed no such correlation, indicating their opportunistic growth in nutrient-limited conditions. This study highlights the significant impact of region-specific hydrographic factors on phytoplankton communities in KCWs, with diatoms dominating in summer and cryptophytes and dinoflagellates showing seasonal and regional variations. Understanding these dynamics is crucial for predicting phytoplankton bloom dynamics and their ecological implications in coastal ecosystems.