The concentrations and fluxes of polychlorinated naphthalenes (PCNs) were measured in surface sediments, and settling particulate matter collected in sediment traps, at two coastal and two offshore sampling stations in the Gulf of Bothnia, northern Baltic Sea, Sweden. The PCN concentrations (of tetra- to hepta-chloro congeners) in the surface sediments ranged from 0.27 to 2.8 ng/g dry weight and were of the same order of magnitude as background concentrations reported previously in Europe. The PCN fluxes in the southern basin (0.93 and 0.86 microg/m2/year) of the Gulf of Bothnia were higher than those in the northern basin (0.58 and 0.49 microg/m2/year); they were also higher near the coast than in the open sea. These PCN fluxes are similar to the pre-industrial levels determined from lake sediments in northwest England. The PCN homologue distribution changed from a relatively even distribution in samples collected near the coast, to TeCNs dominating in the samples from the open sea. This indicates that higher chlorinated PCNs are deposited and retained in sediments to a higher degree near the coast. The total annual deposition of PCNs in sediments in the Gulf of Bothnia was estimated to be 91 kg/year.