Due to influence of wind patterns (monsoon and westerlies) and anthropogenic activities, lower stretch of Himalaya is at direct exposure to persistent organic pollutants (POPs). Current study was designed to monitor atmospheric concentrations of long lived organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) by employing polyurethane foam passive air samplers (PUF-PAS) in Lesser Himalayan Region (LHR) of Pakistan. Levels of ∑HCHs, ∑DDTs and ∑PCBs were observed in a range between 3 and 210 pg m−3, 0.75–67.1 pg m−3 and 8.49–458 pg m−3, respectively. Though, air mass trajectories over LHR indicated long range transport as atmospheric source input which was further explained by Clausius–Clapeyron plots between ln P and inverse of temperature (1000/T; K) where all OCPs and most of the PCBs have shown insignificant relationship (r2 = 5E-06–0.41; p-value = 0.06–0.995). However, local source emissions and valley transport may also implicate based on spatial distribution and altitudinal patterns. Additionally, soil-air partitioning of organochlorines was assessed using octanol-air partition (KOA) and black carbon-air partition (KBC) based models. Regression results indicated combined influence of both organic matter (r2 = 0.298–0.85) and black carbon (r2 = 0.31–0.86) via absorption and adsorption, respectively in soil-air partitioning of OCs in LHR. This paper sheds light on the atmospheric concentrations of OCs and help in better understanding of the processes involved in fate and transport of organic pollutants in Himalayan region. Further investigations are required to understand the role of carbon moieties in fate and transport of other groups of organic pollutants at higher altitudes of Himalayan region.