Plastic barriers physically separate queuing passengers in airport security check areas as a measure against aerosol transmission. However, this may create “canyons” that interfere with the existing ventilation design: potentially inhibiting airflow, concentrating exhaled viruses, and exacerbating aerosol transmission risk. Accordingly, this study investigated the transmission implications of installing plastic barriers in a security check area with computational fluid dynamics (CFD). Two air distribution schemes were modeled: one with linear air supply diffusers aligned vertically to (Case 1) and another with diffusers parallel with (Case 2) the orientation of partitions. The drift-flux model was used to calculate the spread of viral bioaerosols with 5 µm in diameter; then the Wells–Riley equation was applied to assess aerosol transmission risk for SARS-CoV-2. According to simulation results, in Case 1, installing plastic barriers resulted in relatively small changes in volume with a high infection risk of 1% or greater in the breathing zone within the first 25 min. However, in Case 2, using plastic barriers resulted in the continuous increase in this volume within the first 25 min while this volume was near zero if without plastic barriers. In conclusion, installing plastic barriers needs careful consideration because they do not reduce the risk of airborne SARS-CoV-2 transmission and might even exacerbate it without localized ventilation and air cleaning.