Exposure to wastewater treatment system (WWTS)-associated bioaerosols is not only linked with macro/field scale systems but also facilities which are operated in micro- and/or indoor environment such as university campus and research institutions. In this context, investigations on a laboratory-scale WWTS, adopting a sequential batch biofilm process and fed with synthetic municipal wastewater, were done in terms of its global treatment performance and characterization of emitted bioaerosols species. The microbial diversity of captured bioaerosols, collected through conventional particulate matter samplers, was identified on the basis of their metabolic properties using analytical profile index, biochemical tests, and other media specific growth patterns. Monitoring and analysis results of air quality in control and experimental period revealed that particulate emission from bioreactor increased the concentration of PM10 and PM2.5 up to 26.49 ± 4.18 µg/m3 and 12.84 ± 2.48 µg/m3 from an initial level of 17.26 ± 4.58 µg/m3 and 8.70 ± 1.84 µg/m3, respectively. Microscopic observations and staining characteristics revealed that cocci shape gram-negative and bacilli shape gram-positive bacteria dominated the bioaerosols with quantitative contribution as 70% and 9%, respectively. Based on the morphological and biochemical characterization, dominant isolated genera of opportunistic pathogenic bacteria in bioaerosols were identified as Escherichia coli, Bacillus cereus, Bacillus subtilis and Pseudomonas sp. with % dominance as 38.46, 13.46, 9.61 and 25, respectively. Overall, the findings of this study reiterate the concern of biological air pollution in research laboratories and represent an inevitable aspect for the validation of bioaerosol exposure in laboratory-scale WWTS workplaces. © 2022, The Author(s), under exclusive licence to Springer Nature B.V.