Abstract. Air-water exchange fluxes of persistent, bioaccumulative and toxic (PBT) substances are frequently estimated using the Whitman two-film (W2F) method, but micrometeorological flux measurements of these compounds over water are rarely attempted. We measured air-water exchange fluxes of hexachlorobenzene (HCB) and polychlorinated biphenyls (PCBs) on 14 July 2006 in Lake Superior using the modified Bowen ratio (MBR) method. Measured fluxes were compared to estimates using the W2F method, and to estimates from an Internal Boundary Layer Transport and Exchange (IBLTE) model that implements the NOAA COARE bulk flux algorithm and gas transfer model. We reveal an inaccuracy in the estimate of water vapor transfer velocity that is commonly used with the W2F method for PBT flux estimation, and demonstrate the effect of use of an improved estimation method. Flux measurements were conducted at three stations with increasing fetch in offshore flow (15, 30, and 60 km) in southeastern Lake Superior. This sampling strategy enabled comparison of measured and predicted flux, as well as modification in near-surface atmospheric concentration with fetch, using the IBLTE model. Fluxes estimated using the W2F model were compared to fluxes measured by MBR. In five of seven cases in which the MBR flux was significantly greater than zero, concentration increased with fetch at 1-m height, which is qualitatively consistent with the measured volatilization flux. As far as we are aware, these are the first reported ship-based micrometeorological air-water exchange flux measurements of PCBs.