Measurements of polycyclic aromatic hydrocarbons (PAHs) were carried out from 2001 to 2003 in various environmental compartments (ambient air, atmospheric deposition, soils, sediments, runoff, and surface waters) in the Seine Estuary. The goal of this study was to identify the importance of atmospheric fluxes to occurrence of PAHs in the estuary, and to estimate the major pathways of their transport and accumulation within this ecosystem. The annual atmospheric inputs in the estuary ranged from 2.5 to 16 kg for the first sampling year, which is high when compared to those calculated for other European locations. In parallel, PAH transport from the atmosphere to the watershed outlet was investigated for two rural and urban small experimental watersheds within the Seine Estuary. In rural areas, atmospheric inputs are higher than exported loads by surface water and PAHs are accumulating in soils. The inverse occurs in urban areas, where the contribution of atmospheric deposition is negligible compared with PAH exported loads by runoff. These results allowed us to establish a mass balance for PAHs on the scale of the Seine Estuary, and to determine the dynamics of PAH transport. This study highlights the role of the atmospheric compartment in the transfer of contaminants and the importance of the local PAH inputs within the Seine Estuary.