To investigate effects of engineered nanoparticles (ENPs) at environmentally relevant concentrations to aquatic microbial communities, TiO2 at 700 µg/L and ZnO at 70 µg/L were spiked to river water samples either separately or combined. Compared to controls where no ENPs were added, the addition of TiO2 ENPs alone at the tested concentration had no statistically significant effect on both the bacterial and eukaryotic communities. The presence of added ENPs: ZnO or ZnO + TiO2 led to significant shift of the microbial community structure and genus distribution. This shift was more obvious for the bacteria than the eukaryotes. Based on results from single particle-inductively coupled plasma-mass spectrometry (SP-ICP-MS), all ENPs aggregated rapidly in water and resulted in much larger particles sizes than the original counterparts. "Dissolved" (including particles smaller than the size detection limits and dissolved ions) concentrations of Ti and Zn increased, too in treatment groups vs. the controls.