Doam Bay is an estuary where harmful algal blooms (HABs) such as red tides develop frequently in summer. The bay also is influenced by freshwater inflow from Tamjin River in upper regions as well as from an artificial lake in lower regions. Phytoplankton size and species composition were investigated at six stations located in the lower regions in April, June and July, 2007. Physical properties (temperature, salinity and SS) were intensively measured for 3 days (5 occasions) after the freshwater discharges from the dike. The freshwater discharge affected temperature, salinity and turbidity in the study sites adjacent to the freshwater lake. Phytoplankton biomass was larger in April than June and it increased more in July. An explicit shift of species composition was observed. Diatoms were dominant in April and June (>70%) whereas their abundances greatly decreased and chlorophytes increased in July. Pseudo-nitzschia sp. was dominant at all stations (except St. 2) and this change was also detected in ecological indices such as diversity and dominance index.