Compared with dry and wet deposition fluxes, air–water exchange flux cannot be directly measured experimentally. Its model-based calculation contains considerable uncertainty because of the uncertainties in input parameters. To capture the inherent variability of air–water exchange flux of PCBs across the lower Great Lakes and to calculate their annual gross volatilization loss, 57 pairs of air and water samples from 19 sites across Lakes Erie and Ontario were collected using passive sampling technology during 2011–2012. Error propagation analysis and Monte Carlo simulation were applied to estimate uncertainty in the air–water exchange fluxes. Results from both methods were similar, but error propagation analysis estimated a smaller uncertainty than Monte Carlo simulation in cases of net deposition. Maximum likelihood estimations (MLE) of wind speed and air temperature were recommended to quantify the site-specific air–water exchange flux. An assumed 30–40% of relative uncertainty in overall air–water mass transfer velocity was confirmed. MLEs of volatilization fluxes of total PCBs across Lakes Erie and Ontario were 0.78 and 0.53 ng m–2 day–1, respectively, and gross volatilization losses of total PCBs over the whole lakes were 74 kg year–1 for Lake Erie and 63 kg year–1 for Lake Ontario. Mass balance analysis across Lake Ontario indicated that volatilization was the uppermost loss process of aqueous PCBs.