The wide use of carbon nanotubes (CNTs), such as single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs), inevitably causes their release into the environment. Previous studies pointed out that the released CNTs would have negative effects on model animals, plants, or microorganisms. Nevertheless, to date, it is unclear whether the presence of CNTs in wastewater treatment plants (WWTPs) could affect biological nitrogen and phosphorus removal. In this paper, the potential effects of CNTs (SWNTs and MWNTs) on nitrogen and phosphorus removal from real wastewater in an activated sludge system were investigated. It was found that the presence of CNTs had no significant impacts on nitrogen and phosphorus removal even at the exposure concentration of 100 mg L⁻¹. Mechanism studies indicated that the sludge membrane integrity and viability and the respiration of both heterotrophic and autotrophic microorganisms were not affected by CNTs. Further experiments revealed that the presence of CNTs also did not change the transformations of intracellular metabolites (mainly glycogen and polyhydroxyalkanoates) and activities of key enzymes (mainly ammonia monooxygenase, nitrite oxidoreductase, nitrate reductase, nitrite reductase, exopolyphosphatase, and polyphosphate kinase), which was consistent with no observed influences on nitrogen and phosphorus removal.