Great controversy still exists on the ecological effects of silver nanoparticles (AgNPs) especially at relatively low concentrations. The performance, fate of AgNPs and microbiome in CWs were evaluated under a long-term exposure to AgNPs (0, 50 and 200 mu g/L) for 450 days. Results showed that AgNPs (50, 200 mu g/L) caused no obviously negative effects on COD removal whereas nitrogen and phosphorus removals were slightly stimulated. AgNPs could be removed efficiently from wastewater attributed to the accumulations of soil and plant tissues. Mass balance of AgNPs was analysed and soil layer of CWs was the major sink of nanoparticles. High-throughput sequencing further revealed the impact of AgNPs on the ecological structure of CWs. Moreover, the presence of AgNPs altered the relative abundances of key functional bacteria. The ecological risks of persistent exposure to low concentrations AgNPs should not be ignored, even though it did not result in deterioration of the CWs' operating performance in our studies.