The accumulation of pollutants in the semi-enclosed waters of ports has long been a concern. This study assessed the pollution status, sources, and toxicity risks of 16 polycyclic aromatic hydrocarbons (PAHs) in surface sediments of 7 major ports in Taiwan. Total PAHs concentrations in sediments ranged between 8.4 and 572.5 ng/g dw, with an average of 112.4 ± 136.5 ng/g dw. The 3- and 4-ring PAHs (63 %) were the major constituents of PAHs in the sediments. Diagnostic ratios and positive matrix factorization analyses indicated that PAHs in sediments were mainly contributed by biomass combustion (45.0 %), coal combustion (31.5 %), and vehicle emissions and related fossil fuels (23.5 %). The results of ecological risk assessment showed a low–medium risk of PAHs in the sediments outside the port, whereas most of the sediments within the port presented a medium–high risk. An assessment of the possible human health risks indicated that PAHs were present at acceptable levels.