The residual levels of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere and in dissolved phase from Lake Chaohu were measured by (GC–MS). The composition and seasonal variation were investigated. The diffusive air–water exchange flux was estimated by a two-film model, and the uncertainty in the flux calculations and the sensitivity of the parameters were evaluated. The following results were obtained: (1) the average residual levels of all PAHs (PAH16) in the atmosphere from Lake Chaohu were 60.85±46.17ngm−3 in the gaseous phase and 14.32±23.82ngm−3 in the particulate phase. The dissolved PAH16 level was 173.46±132.89ngL−1. (2) The seasonal variation of average PAH16 contents ranged from 43.09±33.20ngm−3 (summer) to 137.47±41.69ngm−3 (winter) in gaseous phase, from 6.62±2.72ngm−3 (summer) to 56.13±22.99ngm−3 (winter) in particulate phase, and 142.68±74.68ngL−1 (winter) to 360.00±176.60ngL−1 (summer) in water samples. Obvious seasonal trends of PAH16 concentrations were found in the atmosphere and water. The values of PAH16 for both the atmosphere and the water were significantly correlated with temperature. (3) The monthly diffusive air–water exchange flux of total PAH16 ranged from −1.77×104ngm−2d−1 to 1.11×105ngm−2d−1, with an average value of 3.45×104ngm−2d−1. (4) The results of a Monte Carlo simulation showed that the monthly average PAH fluxes ranged from −3.4×103ngm−2d−1 to 1.6×104ngm−2d−1 throughout the year, and the uncertainties for individual PAHs were compared. (5) According to the sensitivity analysis, the concentrations of dissolved and gaseous phase PAHs were the two most important factors affecting the results of the flux calculations.
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