Abstract The Seine River basin (France) is representative of the large urbanised catchments (78,650 km 2 ) located in Northwestern Europe. As such, it is highly impacted by anthropogenic activities and their associated emissions of pollutants such as polycyclic aromatic hydrocarbons (PAHs). These compounds, originating from household heating and road traffic, are responsible for serious environmental issues across the basin. This study aims at establishing and using mass balance analyses of PAHs at the Seine River basin scale as an efficient tool for understanding PAH pathways in the environment. A dual-scale approach (urban vs. rural areas) was used successfully, and mass balances provided useful knowledge on the environmental fate of PAHs. In urban areas, runoff and domestic and industrial discharges contributed similarly to the PAH supply to the sewer system. During the wastewater treatment process, PAHs were mainly eliminated through sludge removal. At the basin scale, substantial amounts of PAHs were quantified in soils, and the limited annual inputs and outputs through atmospheric deposition and soil erosion, respectively, suggest that these compounds have long residence times within the basin. While wastewater and runoff discharges from urban areas account for a substantial part of PAH urban fluxes to the Seine River, soil erosion seems to be the predominant contributor at the basin scale. Overall, the PAH flux at the basin outlet was greater than supplies, suggesting that the Seine River system may currently be undergoing a decontamination phase.