The detection of biological aerosol particles (bioaerosols) is relevant to many scientific fields. The mechanisms responsible for inactivating airborne microorganisms in the atmosphere may also impact their detection and measurement. This work aims to determine the effect of aerosol generation and filter air sampling on bacterial viable counts and DNA concentration and quality. Aerosols of Escherichia coli MRE162 and Pseudomonas putida NCTC10936 were generated into HEPA-filtered air, within a linear wind tunnel, for either 10 seconds or 20 minutes. Bioaerosols were sampled using glass-microfibre filters for either 10 minutes (short-term sampling) or 5 hours (long-term sampling). Relative humidity and temperature were monitored throughout. Bacteria were eluted from the filters and quantified using viable counts following overnight incubation. The remaining buffer was centrifuged to pellet the bacteria, and DNA was extracted following a standard DNA extraction protocol. DNA quality and concentration were determined using the TapeStation 4200 instrument and Qubit 4 reader. Although short-term air sampling had minimal effect on the viable counts of E. coli, it led to a significant reduction in P. putida counts. Sampling for extended periods, however, led to a significant reduction in viable counts for both bacterial species. The duration of air sampling had minimal impact on DNA concentration, however, the degree of DNA fragmentation significantly increased after 10 minutes of air sampling. Future work will determine the impact of filter air sampling on Polymerase Chain Reaction and third-generation sequencing techniques. This information will inform bioaerosol detection practices for human, animal and plant health and biodefence.