Nanomaterials present in wastewater can pose a significant threat to aerobic granular sludge (AGS) systems. Herein, we found that compared to graphene nanomaterials (G-NMs), the long-term presence (95 days) of graphene oxide nanomaterials (GO-NMs) resulted in an increased proliferation of filamentous bacteria, poorer sedimentation performance (SVI30 of 74.1 mL/g) and smaller average particle size (1224.4 µm) of the AGS. In particular, the GO-NMs posed a more significant inhibitory effect to the total nitrogen removal efficiency of AGS (decreased by 14.3 %), especially for the denitrification process. The substantial accumulation of GO-NMs within the sludge matrix resulted in a higher level of reactive oxygen species in AGS compared to G-NMs, thereby inducing lactate dehydrogenase release, and enhancing superoxide oxidase and catalase activities. Such excessive oxidative stress could potentially result in a significant reduction in the activity of nitrogen metabolism enzymes (e.g., nitrate reductase and nitrite reductase) and the expression of key functional genes (e.g., nirS and nirK). Altogether, compared to G-NMs, prolonged exposure to GO-NMs had a more significant chronic toxicity effect on AGS systems. These findings implied that the presence of G-NMs and GO-NMs is a hidden danger to biological nitrogen removal and should receive more attention.