This study investigates the seasonal and spatial differences in phytoplankton communities in the coastal waters off two nuclear power plants in northern Taiwan in 2009. We identified 144 phytoplankton taxa in our samples, including 127 diatoms, 16 dinoflagellates, and one cyanobacteria. Four diatoms, namely, Thalassionema nitzschioides (T. nitzschioides), Pseudo-nitzschia delicatissima (P. delicatissima), Paralia sulcate (P. sulcata), and Chaetoceros curvisetus (C. curvisetus) and one dinoflagellate Prorocentrum micans (P. micans) were predominant during the study period. Clear seasonal and spatial differences in phytoplankton abundance and species composition were evident in the study area. Generally, a higher mean phytoplankton abundance was observed in the waters off the First Nuclear Power Plant (NPP I) than at the Second Nuclear Power Plant (NPP II). The phytoplankton abundance was usually high in the coastal waters during warm periods and in the offshore waters in winter. The phytoplankton species composition was different in the NPP intake and outlet. An abundant phytoplankton increase in the outlet was frequently detected, probably due to the difference in phytoplankton species suitability to thermal stress. Our results suggest that thermal discharge may affect the phytoplankton communities by altering its species composition within a restricted area close to the NPP. This study provides basic knowledge on phytoplankton distribution patterns, essential information required to further understand the ecological impact caused by thermal effluents.