Environmental factors and changes in phytoplankton community structure before (August 5, 2017), during (August 18 and 25) and after (August 30 and September 15) freshwater input were analyzed to investigate the effects of freshwater input from Ganwol and Bunam lakes located in the upper part of Cheonsu Bay. Due to the large amount of freshwater input in the Cheonsu Bay, the surface salinity of the bay decreased by more than 8 psu, and the thermocline existing in the bay during August weakened. In addition, hypoxic phenomena occurred temporarily in the bay as the low oxygen water mass from the freshwater lakes flowed into the bay, and chemical oxygen demand, nutrients, and N/P increased with freshwater inflow. The density of phytoplankton during the freshwater inflow increased owing to their input from the freshwater lakes. Diatom species (Eucampia zodiacus) dominated the phytoplankton community in the bay before freshwater input; nanoflagellates, chlorophyta, cyanobacteria, and diatoms (Pseudonitzschia delicatissima, Chateocceros spp.) entered during freshwater input; and after freshwater inflow ended, diatoms (Chateocceros spp.) again became predominant indicating a return to previous conditions. The amount of phytoplankton standing crops increased sharply due to the inflow of freshwater species into the bay on the second day of discharge compared to before freshwater input; pre-discharge conditions were restored at most stations except at some sites close to the Bunam Lake three days after discharge. Therefore, the large amount of freshwater flowing into the bay affects not only the geochemical circulation in the bay but also the phytoplankton community structure. In particular, the high concentration of nutrients in the freshwater lake affect the marine ecosystem of the bay during August.