Polycyclic aromatic hydrocarbons (PAHs) in semi-enclosed gulfs are influenced by physical and biochemical processes, which haven’t been well understood. This study aims to investigate the spatial distribution and vertical profiles of dissolved PAHs in the Beibu Gulf and adjacent waters of the South China Sea, along with hydrological, meteorological, and biochemical variables. Particularly relevant are the effects of atmospheric pressure, salinity, ammonium, chlorophyll-a, as well as riverine inputs (RI), sea currents, and upwelling. In surface seawater, the total concentrations of eight dissolved PAHs (∑8PAHs) were 7.76 ± 2.16ng/L, with a distribution pattern of western Guangdong waters (WGWs) > BG > Qiongzhou Strait (QS). ∑8PAHs in the northern BG (9.10 ± 2.00ng/L) was significantly higher than that in the southern BG (6.65 ± 1.54ng/L) (p < 0.01), suggesting that local anthropogenic activities and unique environmental characteristics significantly influenced PAHs distribution. In water column, PAHs in BG displayed enrichment in surface and bottom but decreased in medium water, while those in WGWs and QS decreased with increasing depth. Source apportionment concluded that PAHs in QS and WGWs were primarily from petroleum sources, and PAHs in BG were mainly from coal combustion. RI, combined with circulation, coastal current, and intrusion of SCS water influenced the surface PAHs distribution in BG, with eddy impacts observed. Specifically, regarding the surface PAHs distribution, differences in atmospheric pressure may influence the air-sea exchange of PAHs, especially positively affecting 4-ring PAHs. Salinity factors further corroborated the contribution of RI to 3-ring PAHs, followed by the regulation of PAHs through biological pumps (ammonia and chlorophyll-a). Moreover, upwelling-induced biodegradation and resuspension affected the vertical distribution of PAHs. While most PAHs posed a negligible risk, coking-generated fluorene posed a moderate risk to ecosystems due to changes in the energy structure, warranting further investigation into its toxicological impacts.