Polycyclic aromatic hydrocarbons (PAHs) were analyzed to elucidate the distribution, ecological risk, pathways, and fluxes of these pollutants in and around the Seto Inland Sea, an industrialized coastal region of Japan. High molecular weight PAHs (5–6 rings) were primarily found in regions close to the bay estuaries, and their proportions decreased at distances further from the estuaries (offshore areas), where low molecular weight PAHs (2–4 rings) were more ubiquitous. Screening-level risk assessments revealed that the PAHs found in the sediments should have no adverse effects on benthic communities. A mass balance for PAHs in the Seto Inland Sea, calculated based on data collected in the field and published literature findings, showed the PAH flux into the Seto Inland Sea from atmospheric deposition were ca. 6 times higher than that from riverine inflows. Comparison of the amount of the PAH mass flux between the Seto Inland Sea and the sea of the Europe and Asian countries indicated that the Seto Inland Sea is less polluted than the Gulf of Lion, the Mediterranean Sea, and the Bohai Sea, China and more polluted than the Yellow Sea. This paper is the first to determine the fluxes of PAHs in the coastal region of Japan.