Increasing release of nanoplastics (NPs) into wastewater may pose a potential threat to nitrogen and phosphorous removals in ecological wastewater treatment systems. To better understand the responses of bioretention system (BRS) by NPs, a Conventional Sand BRS (CB-BRS) and two modified BRSs, Microbial Fuel Cell (MFC)-Biochar BRS (MB-BRS) and Pyrolusite-MFC-Biochar BRS (PMB-BRS) were established and the effects of 0.5 mg/L polymethyl methacrylate (PMMA) NPs on nutrient removal, microbial community structures, as well as key enzyme activities, functional genes, antibiotic resistance genes (ARGs) were comprehensively investigated within a 120-day exposure. We observed a significant decrease in total nitrogen (TN) and total phosphorous (TP) removals in BRSs. TN removal efficiencies gradually declined from 93.56 % to 54.23 % and the TP removal efficiencies declined from 88.29 % to 74.47 % in CB-BRS. By contrast, MB-BRS (TN:72.28 %; TP:81.58 %) and PMB-BRS (TN:80.76 %; TP:96.69 %) apparently overperformed CB-BRS. In conjunction with ecological-relevant functional prediction based on the FAPROTAX database, the Illumina high-throughput sequencing unveiled substantial selective pressure imposed by PMMA NPs, particularly leading to diminished denitrifying microbes. PMMA NPs adversely affected key nitrogen-transformation enzyme activities (URE, AMO, and NIR) and denitrification functional genes (nirK, nirS, and nosZ). Alarmingly, PMMA NPs stimulated ARGs (sulI and tetC) propagation in all BRSs. Notably, the introduction of pyrolusite and biochar mitigated the adverse effects through the formation of manganese cycle and prosperous electron transfer process and effectively retained ARGs after 120-day exposure. The findings provide unprecedented insights into the potential ecological threat posed by PMMA NPs and viable strategies to control this hidden danger.