The blue swallow (Hirundo atrocaerulea) is one of the most threatened bird species in southern Africa. Among terrestrial birds, its plumage is known to be the most water repellent, an adaptation to foraging on the wing in dense fog. Despite this unique adaptation, the nesting success of the blue swallow at the Blue Swallow Natural Heritage Site (BSNHS) is lower during years with high incidence of fog. As the phenomenon is not observed at other nesting sites, we hypothesized that this is due to changes in the air chemistry at the BSNHS. In the immediate proximity of the BSNHS, plantations of exotic trees (e.g., pines and eucalypts), rich in volatile organic compounds (VOCs), are dominant features. In addition, air pollution from the Johannesburg area is transported with the surface winds and mix with VOCs released from exotic trees. Together with the high humidity and high elevation, these conditions may result in the formation of sulphonates. Sulphonates are strong detergents, and the presence of these in the fog could lead to decreased water repellence of the plumage. This study was performed in order to determine the occurrence and distribution of sulphonates in the BSNHS and to compare these with sulphonates formed in other locations in South Africa. Because the blue swallow is endangered, pine needles were used as proxy to detect formation of sulphonates. We sampled pine needles with different exposure to air pollutants, in climates with different humidity, and at different elevation and analyzed these for sulphonates using mass spectrometry. Pine needles from high elevations and the BSNHS, with high humidity, and exposure to air pollution contained significantly higher concentrations of sulphonates than pine needles from low elevations or from high elevations with a dryer climate or a different combination of air pollutants. These findings lead to two conclusions. First, the occurrence and distribution of sulphonates may be explained by chemical reactions between sulphur dioxide and organic compounds in the humid air induced by ultraviolet radiation. Second, elevated concentrations of sulphonates in the fog could affect the water repellence of the blue swallow plumage, possibly decreasing their capacity to forage in the fog. We cannot prove conclusively that this is the reason why the number of blue swallows at the BSNHS has decreased dramatically, but for endangered species, we may have to rely on proxies to draw conclusions about outside threats. All such information should be valuable in devising protection plans for species under threat. The use of proxies to elucidate threats to endangered species should be evaluated in a broad scale. The mist-belt habitat in general is threatened by many human activities. These findings indicate that air pollution and the proximity of volatile organic compound (VOC) sources close to mist-belt habitat refuges may be an unrecognised conservation threat to the animals inhabiting them.