Wastewater treatment plants (WWTPs) play important roles in water purification but are also important source of aerosols. However, the relationship between aerosol characteristics and wastewater treatment process remains poorly understood. In this study, aerosols were collected over a 24-month period from a WWTP using a modified anaerobic-anoxic-oxic process. The aerated tank (AerT) was characterized by the highest respiratory fraction (RF) concentrations (861–1525 CFU/m3) and proportions (50.76%–65.96%) of aerosol particles. Fourteen core potential pathogens and 15 toxic metal(loid)s were identified in aerosols. Mycobacterium was the genus that aerosolized most easily in fine grid, pre-anoxic tank, and AerT. High wastewater treatment efficiency may increase the emission of RF and core potential pathogens. The median size of activated sludge, richness of core potential pathogens in wastewater, and total suspended particulates were the most influential factors directly related to the RF proportions, core community of potential pathogens, and composition of toxic metal(loid)s in WWTP aerosols, respectively. Relative humidity, temperature, input and removal of biochemical oxygen demand, dissolved oxygen, and mixed liquor suspended solids could also directly or indirectly affect the aerosol characteristics. This study enhances the mechanistic understanding of linking aerosol characteristics to treatment processes and has important implications for targeted manipulation.