We investigated the influence of the Changjiang diluted waters (CDW) on the distribution of nanophytoplankton (<20 µm) abundance and biomass in the northern East China Sea (ECS) during two research cruises conducted in the summers of 2010 and 2012, using flow cytometry. Each group of nanophytoplankton responded differently to the distribution of the CDW. In the surface layer, Synechococcus 1 which has low orange fluorescence, a major component of summer nanophytoplankton, were more abundant under the large extension of CDW to the northern ECS in August 2010, whereas the abundance of other groups including Synechococcus 2 which has high orange fluorescence, and pico- and nano-eukaryotes (0.2–2 and 2–20 µm in diameter, respectively), dramatically increased under the small extension of CDW in August 2012. The subsurface chl-a maximum layer became more developed under the small extension of CDW, and was dominated by nano-eukaryotes. During two study periods, environmental characteristics in the CDW also showed annual variations, with higher seawater temperature, lower salinity, and higher nitrate concentration in the surface layer of the CDW in August 2010. The summer distributions of Synechococcus and nano-eukaryotes were likely to be limited by low salinity and high temperature, respectively, indicating that phytoplankton distribution could be influenced not only by the extension level of the CDW but also by the change of the environmental characters of the CDW.