Sea microlayer (SML) and subsurface water (SSW) samples were collected around Xiamen Island to study the enrichment and partitioning of polycyclic aromatic hydrocarbons (PAHs). Total PAH concentrations ranged from 93.43 to 411.05ng L−1 in the SML and 49.29–279.42ng L−1 in the SSW. Compared with the results of previous studies before pollution control measurements, PAHs levels decreased significantly. The enrichment factors (EFs) of dissolved and particulate PAHs varied from 0.68 to 2.71 and 0.43–3.56. EFs showed the consistent enrichment trends with sites and exhibited different enrichment characteristics between 2 and 3 ring PAHs and 4 ring PAHs. Furthermore, the much higher concentrations of BaP (strong carcinogenicity) were accompanied by higher EFs in the SML samples from the Western Xiamen Harbour, which together indicated the risk of impacts to the fish eggs that usually float on the SML water after exposure to oil spills and combustion, contributed directly by the port and shipping activities.