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A naval ship's exhaust gas scrubber may discharge polycyclic aromatic hydrocarbons (PAHs) into seawater. Due to the high lipophilicity and low water solubility of PAHs, their concentrations in seawater are extremely low, making them difficult to detect or accurately determine. To accurately assess the impact of scrubber washwater effluent on the PAHs concentration of seawater, appropriate analysis methods must be established. In this study, a large-volume pre-concentration water sampler was used onboard to concentrate PAHs in surface seawater (100 L) from four sites offshore of southern Taiwan. The quantitative and qualitative analysis of dissolved PAHs in seawater and quality control samples were implemented using a GC/MS system with the aid of internal and surrogate standards. Results showed that the field and equipment blank samples of quality control samples were lower than twice the detection limit. The detection limit of individual PAHs is between 0.001 (naphthalene, NA) and 0.014 ng/L (dibenzo[a,h]anthracene, DBA), which meets the requirements for evaluating PAHs in seawater (that is, less than the maximum permissible concentrations (MPCs)). The concentration of total PAHs (TPAHs) in the four seawater samples ranged from 2.297 to 4.001 ng/L and had an average concentration of 3.056 ± 0.727 ng/L. The concentrations of 16 PAHs were determined in each seawater sample, indicating that the analytical method in this study is suitable for the determination of low-concentration PAHs in seawater. Phenanthrene (PHE) is the most dominant compound in seawater samples accounting for 59.6 ± 12.6% of TPAHs, followed by fluorine (FL) accounting for 8.5 ± 3.7%. The contribution of high-ring PAHs to TPAHs is not high (0.5–9.2%), but the observed concentrations can cause a higher risk to aquatic organisms than low-ring PAHs. The diagnostic ratio showed that the sources of PAHs in the seawater collected offshore of southern Taiwan may include mixed sources such as petrogenic, petroleum combustion, and biomass combustion. The results can be used for regular monitoring, which contributes to pollution prevention and management of the marine environment. [ABSTRACT FROM AUTHOR]