The fate and behaviour assessment of ZnO- and Ag-engineered nanoparticles (ENPs) and bacterial viability in a simulated wastewater treatment plant (WWTP) fed with municipal wastewater was investigated through determination of ENPs stability at varying pH and continuous exposure of ENPs to wastewater, respectively. The ENPs were introduced to a 3-L bioreactor (simulated WWTP) with a hydraulic residence time (HRT) of 6 h at a dose rate of 0.83 mg/min for 240 h. The stability of the ENPs was found to be dependent on their dissolution and aggregation at different pH, where ZnO ENPs exhibited the highest dissolution at low pH compared to Ag ENPs. The results also showed that both ENPs had high affinity for the sewage sludge as they undergo aggregation under typical wastewater conditions. Results of effluent monitored daily showed mean COD removal efficiencies of 71 ± 7% and 74 ± 8% for ZnO and Ag ENPs in test units, respectively. The treated effluent had low mean concentrations of Zn (1.39 ± 0.54 mg/L) and Ag (0.12 ± 0.06 mg/L); however, elevated mean concentrations of Zn (54 ± 39 mg/g dry sludge) and Ag (57 ± 42 mg/g dry sludge) were found in the sludge - suggesting removal of the ENPs from the wastewater by biosorption and biosolid settling mechanisms. Using X-ray diffraction (XRD) and transmission electron microscopy (TEM), the mineral identities of ZnO and Ag ENPs in the sludge from the test units were found comparable to those of commercial ENPs, but larger due to agglomeration. The bacterial viability assessment after exposure to ENPs using the Live/Dead BacLight kit, although not quantitatively assessed, suggested high resilience of the bacteria useful for biodegradation of organic material in the simulated wastewater treatment system.