Experimentally determined octanol–air partition coefficients (KOA) for 43 polychlorinated naphthalene (PCN) congeners and experimentally determined subcooled liquid vapor pressures (PL) for 17 PCN congeners were used with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to generate three-dimensional quantitative structure–activity relationship (3D–QSAR) models. The data were used to predict KOA values for the other 32 congeners and PL values for the other 58 congeners. The CoMFA and CoMSIA model contour maps showed that the electrostatic fields of the PCN molecules are the most important factors affecting the KOA and PL values. The long-range transport potentials of several PCN homologs were assessed using the following grading system: high mobility (MoCNs), relatively high mobility (DiCNs to TeCNs), relatively low mobility (PeCNs to HeCNs) and low mobility (HeCNs and OCN). The PCN-2 molecule was modified using the contour maps of the two models, and the results showed that introducing an electronegative R1 substituent increased the KOA value but introducing an electropositive R6 substituent decreased the PL value. PCN-2 was in the high mobility class, but introducing these substituents moved the long-range transport potentials of the modified molecules to the relatively high mobility class.