The reactor performance, granules characteristics and microbial population dynamics were investigated to assess the chronic responses of aerobic granules to zinc oxide nanoparticles (ZnO NPs) of 0, 5, 10 and 20 mg/L for a period of 180 days. The results showed that ZnO NPs stimulated COD removal, whereas caused inhibition to both nitrification and denitrification. However, biological phosphorus removal remained effective and stable. Introduction of ZnO NPs sharply decreased the respiration of granules, while did not change the settleability. Both content of extracellular polymeric substances (EPS) and the ratio of protein to polysaccharides (PN/PS) rose significantly. MiSeq pyrosequencing was employed to explore the microbial population dynamics. Results demonstrated that up to 20 mg/L reduced the alpha-diversity of bacterial communities. Finally, phylogenetic classification of the dominant functional species involved in biological nutrients removal were identified to assess the effects of ZnO NPs to aerobic granules from the molecular level. (C) 2017 Elsevier Ltd. All rights reserved.