The extensive use of silver nanoparticles (Ag NPs) inevitably leads to their release into aquatic ecosystems through sewage discharge. Currently, the impact of Ag NPs on activated sludge has been widely reported, however little is known about how Ag NPs influence nitrogen transformation and metabolic pathways in biofilm systems. In this study, the effects of Ag NPs on nitrogen transformation in constructed wetlands (CWs) were studied using metagenomic analysis. Results showed that total nitrogen and ammonia-nitrogen removal rates were significantly lowered after short-term exposure (5 d) to 1 and 50 mg/L Ag NPs, and long-term exposure (60 d) to Ag NPs caused cumulatively inhibitory effects on nitrogen removal. In addition, the majority of Ag NPs were captured by the CW substrate, with minor amounts reaching plant tissues and effluent. Scanning electron microscopy images and lactate dehydrogenase release assays suggested that a large number of NPs were adsorbed onto the biofilms covering the gravel, which significantly inhibited microbial viability. Furthermore, metagenomic analysis revealed that, bacterial community structures were significantly altered by the presence of Ag NPs, especially those of nitrogen-transforming microorganisms. Clusters of Orthologous Groups annotation demonstrated that Ag NPs impacted metabolic functional potentials, especially for amino acid transport and metabolism. Kyoto Encyclopedia of Genes and Genomes annotation indicated that Ag NPs changed the nitrogen metabolic pathways. Overall, Ag NPs resulted in a decline in the nitrogen removal rate in CWs, which is likely to cause eutrophication of receiving waters.