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 bacterial and fungal concentrations in a WWTP in southwestern Iran between September 2015 and May 2016. Active sampling was conducted around operational units, and a total of 600 bacterial and fungal samples were collected. Spatial and seasonal comparisons were made. The highest average concentrations of culturable bacterial aerosol at seasonally dependent locations were, in decreasing order, 2581 ± 401 and 1952 ± 390 CFU m–3 for the selector and aeration tanks, respectively, in autumn; 1363 ± 299 CFU m–3 for the aeration tank in winter; and 1738 ± 350 CFU m–3 for the screw pump in spring. Furthermore, the predominant genera of airborne fungi isolated from the air of the WWTP in all three seasons were Cephalotrichum spp., Alternaria spp., Penicillium spp., Monilia spp., and Aspergillus spp. The results of this work emphasize the necessity of controlling WWTP workers’ exposure to bioaerosols when bacteria and fungi become aerosolized during aeration.