In order to investigate the fluctuation rates [FR] of phytoplankton after passage through a cooling system, the standing crops, chlorophyll a concentrations and carbon assimilation number of phytoplankton were surveyed at intake and outlet at Wolsong nuclear power plant [NPP] from July 2006 to June 2008. As a result, the total mean standing crops of phytoplankton were 1.0 ×106 cells L-1 and 7.3×105 cells L-1 at intake and outlet, respectively. The FR of phytoplankton by passage through the cooling system [PTCS] was 27.0%. Among them, the FR of microplankton and nanoplankton were 34.1% and 12.4%, respectively. In addition, the FR of diatoms and dinoflagellates were 33.9% and 29.7%, respectively. These results showed the entrainment effects on microplankton and diatoms by PTCS were higher than those of nanoplankton and dinoflagellates. The FR of total chlorophyll a concentrations were 54.4%, and the FR of microplankton, nanoplankton and picoplankton were 58.9%, 38.5%, and 52.4%, respectively. So the entrainment effects on microplankton by PTCS were higher than those of nanoplankton and picoplankton. The mean FR of carbon assimilation number of phytoplankton was 57.6%, and the seasonal variations of FR of carbon assimilation number ranged from 47.5% to 76.8%. Our results indicated that the phytoplankton species responded differently to power plant operating conditions such as elevated temperature, chlorination, and mechanical impacts.