Bioaerosols produced from Wastewater Treatment Plants (WWTPs) can pose health risks to plant workers and nearby inhabitants. There is a gap in air quality data for WWTPs in developing countries. The present study aimed to measure airborne bacteria and fungi concentrations in a WWTP in southwestern Iran between September 2015 and May 2016. Active sampling was carried out around operational units and a total of 600 bacterial and fungal samples were collected. Spatial and seasonal comparisons were made. Seasonally-dependent locations for the highest concentration of culturable bacterial aerosol were as follows: selector and aeration tanks exhibited an average of 2581 ± 401 and 1952 ± 390 CFU m-3 in autumn, respectively; the aeration tank had an average of 1363 ± 299 CFU m-3 in winter; and the screw pump exhibited an average of 1738 ± 350 CFU m-3 in spring. Furthermore, the predominant genera of airborne fungi isolated from the air of the WWTP in the three seasons were Cephalotrichum spp., Alternaria spp., Penicillium spp., Monilia spp., and Aspergillus spp. The results of this work emphasize the necessity to control WWTP workers’ exposure to bioaerosols when airborne bacteria and fungi become aerosolized during aeration.