The understandings of environmental activities and regional inventory of ship stack PAHs are very limited in Shanghai due, in part, to the lack of source-segregated analysis. To address this, measured PAHs in organic film on ship surfaces were employed to reconstruct concentrations in various compartments through a fugacity model to investigate the level, transport, fate and annual emission of ship stack PAHs in Shanghai. The results revealed that ship stack PAHs results in 11.2–181 ng L−1 and 71.0–1710 ng g−1 in water and sediment of Shanghai, respectively. After being released into air, ship stack PAHs mainly concentrated in organic films and sediments while sunk in water and sediment. Crucial mass transfer pathways include deposition of airborne and sediment PAHs. The mass loss of ship stack PAHs was primarily through air advection, followed by degradation in sediment. The ship emissions (53.7 tons annually) accounted for approximate one tenth of the regional total in Shanghai (in 2017). Additionally, shipping was estimated to release 127 tons of PAHs annually into the Shanghai section of Yangtze River. Our results suggest our fugacity-based approach can be used to estimate the regional emissions and inventory of ship stack PAHs in the surrounding environment.