Although TOC removal was not evidently affected by Ag-NPs, significant decrease in nitrifying activity (from 98% to about 15%) was observed in the OMBR. Ag-NPs also caused remarkable increase of EPS from 95.7 to 170.1 mg/gMLVSS, mostly contributed by the increase in protein content. A major shift in the bacterial community structure and decrease in community diversity was also revealed in 16S rRNA gene based PCReDGGE analysis.