Engineered nanoparticles (ENPs) have shown invaluable societal benefits and applications in drug targeting, biological imaging and industrial products. ENPs enter the water body through various paths during the processes of production, usage and emission, therefore the behavior and the biosafety of ENPs in water bodies have attracted increasing attention. As the primary producer of ecosystems, phytoplankton provide nutrients, energy and oxygen for both themselves and organisms at higher trophic levels in the aquatic ecosystems. These primary producers may be exposed to the biological and unpredictable effects of this emergent pollutant to the aquatic ecosystems. Numerous studies have proved the toxic effects of ENPs on phytoplankton, but the mechanisms of entry into the aquatic organisms as well as the stability, fate and biotransformation in phytoplankton still remain unclear. Here, we present a review of the pathways of ENPs entering the water, the subsequent behavior and biological effects of ENPs on phytoplankton with an emphasis on latest findings and current knowledge. Future research and endeavors shall focus further on the understanding of mechanisms, fate and transport of ENPs in the aquatic ecosystems.