The contents of 16 polycyclic aromatic hydrocarbons (PAHs) and surface sediment properties were analyzed from 31 locations in Dapeng Bay and neighboring rivers (i.e., Kaoping River, Tungkang River, and Lingbeng River) in Taiwan. Principal component factor analysis (PCFA) showed that the most important latent factors are the soil-texture-caused factor, the PAHs-caused factor, and the nutrient-caused factor. Contour maps incorporating factor scores showed that phenanthrene and pyrene of PAHs had the highest content at the entrance of the northern side of the lagoon. Benzo(a)pyrene had the highest content located in the midsection of the Kaoping River and in Dapeng Bay. Moreover, canonical discriminant analysis shows that sediment quality in Dapeng Bay was not similar to the other three rivers. The methodologies and results provide useful information on watershed management and may be applicable to other basins with similar properties that are experiencing similar coastal environmental issues.