Bulk atmospheric deposition fluxes, air-water exchange fluxes, particle settling fluxes out of the upper water column, sediment trap fluxes in deep waters, and sediment burial fluxes of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were simultaneously measured in the Koster Fjord, eastern Skagerak, on the Swedish west coast. The aim of the study was to compare the magnitude and direction of the compound fluxes in the system in order to diagnose key fate processes. The PCB and PAH fluxes via net atmospheric deposition, settling particles out of the surface and through deep waters, as well as into the accreting underlying sediments were shown to be remarkably similar, agreeing within a factor of a few for any given target compound. Fluxes of all PCB and PAH target compounds remained fairly constant with water column depth. Thus, there was no evidence for net desorption from sinking particles. The net unidirectional and near balancing of vertical fluxes suggests a net transport of PCBs and PAHs from the atmosphere to the continental shelf sediments in the Koster Fjord, which is consistent with the hypothesis that the shelf sediments are important sinks for these compounds.