This study reports the first investigation of polychlorinated naphthalenes (PCNs) in air and soil samples from ecologically important sites of the Indus River Basin, Pakistan. The concentrations of ∑39-PCNs in air and soil were found in a range between 1–1588 pg m−3 and 0.02–23 ng g−1 while the mean TEQ values were calculated to be 5.4E−04 pg TEQ m−3 and 1.6E+01 pg TEQ g−1, respectively. Spatially, air and soil PCN concentrations were found to be high at Rahim Yar Khan (agricultural region). Lower-medium chlorinated PCNs (sum of tri-, tetra- and penta-CNs) predominated in both air and soil, altogether constituting 87 and 86% of total PCNs in the two environmental matrices, respectively. According to the data, soil–air partitioning of PCNs was interpreted to be similarly controlled by the combined effect of black carbon and organic matter in the Indus River Basin, with no preferential implication of the recalcitrant organic form.