To understand the changes in physical parameters and phytoplankton size structure caused by tides, a fixed station in the Youngsan River estuary was monitored at 2-h intervals, on April 28, 2012 and August 12, 2012. No clear relationship was observed between the temperature and salinity changes and tidal levels in April. However, in August, temperature decreased during the ebb tide and increased during the flood tide, while salinity showed the opposite trend. In addition, there was no specific change in the phytoplankton biomass corresponding to tidal levels in April. In August, the total chlorophyll a and the biomass of net phytoplankton (>20μm ) increased almost 20 times during the ebb tide and decreased during the flood tide. The biomass of nanophytoplankton (<20μm ) showed a similar variation in response to tidal level changes. In April, the relationship between percent contributions of phytoplankton size structure and tidal levels was not clear. In August, the net phytoplankton was dominant in the early stage and nanophytoplankton was dominant in the later stage, while contribution of nanophytoplankton and net phytoplankton increased at high tide and low tide, respectively. Therefore, in April, other factors such as freshwater discharge were more important than the tide, whereas in August, when no freshwater discharge was recorded, the changes in semidiurnal tides influenced the physical parameters and phytoplankton dynamics. These results could contribute to the understanding of phytoplankton dynamics in the Youngsan River estuary.