Multiple environmental variables related to ocean currents, freshwater runoff, and upwelling in a coastal area have complex effects on the phytoplankton community. To assess the influence of environmental variables on the phytoplankton community structure during the summer of 2019, we investigated the various abiotic and biotic factors in Korean coastal waters (KCWs), separated into five different zones. Summer environmental factors in KCWs were strongly influenced by Changjiang Diluted Water (CDW) in St. SO (Southern Offshore) 1 and 2, upwelling in St. SI (Southern Inshore) 2–4, and Nakdong River discharge in St. SI 12. In particular, low–salinity water masses (p < 0.05 for nearby locations) of CDW gradually expanded from the East China Sea to southwestern KCWs from June to July. In addition, there were high levels of nutrients following freshwater runoff from the Nakdong River in southeastern KCW, which led to the dominance of Cryptomonas spp. (81%), a freshwater and brackish water algae. On the other hand, upwelling areas in southwestern KCW were dominated by diatoms Skeletonema spp., and are characterized by high phosphate concentrations (p < 0.05) and low temperatures (p < 0.05) compared to nearby locations. Leptocylindrus danicus (20%) was dominant due to the effect of water temperature in the SE (Southeastern area) zone. Low nutrient concentrations were maintained in the East Sea (dissolved inorganic nitrogen (DIN) = 0.39 ± 0.40 μM; dissolved inorganic phosphate (DIP) = 0.09 ± 0.03 μM) and the Yellow Sea (DIN = 0.40 ± 0.07 μM; DIP = 0.04 ± 0.02 μM), which were characterized by low levels of chlorophyll a and dominated by unidentified small flagellates (35, 40%). Therefore, our results indicated that hydro–oceanographic events such as upwelling and freshwater run–off, but not ocean currents, provide nutrients to the euphotic layers of the coastal environment and play important roles in determining the phytoplankton community structure during summer in the KCWs.