In this study, the effect of Chlamydomonas reinhardtii on the fate of CuO nanoparticles (CuO-NPs) in aquatic environment were investigated in terms of the colloidal stability, the free Cu releasing, extracellular adsorption Cu (Cu) and intracellular assimilation Cu (Cu). The results showed that, with the increasing microalgal density, the absolute value of zeta potential of CuO-NPs decreased and the mean hydrodynamic diameter (MHD) became larger, leading to a better aggregation and settling behavior of CuO-NPs. The microalgae also promoted the free Cu releasing, however, inhibited adsorption and assimilation of metal nanoparticles (MNPs) into microalgal cells, resulting in the reduction of the Cu and Cu per microalgal cell. The phenomenon was probably due to the reduced chance of contact between microalgae and MNPs. The internalization of CuO-NPs was also observed in microalgal cells by high resolution transmission electron microscope (HRTEM). Furthermore, the results of fast fourier transform (FFT)/inversed FFT (IFFT) analysis indicated that the CuO-NPs was reduced to CuO-NPs in the microalgae cells. The above results suggested that the microalgae can significantly affect the fate of MNPs, and subsequently, influencing the bioavailability and toxicity of MNPs in the aquatic environment.