This study investigated the concentrations of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) in the particulate and dissolved phase, as well as concentrations of PAHs in the sediment in Kaohsiung Harbor lagoon. Sources of PAHs in the water column were determined by isomer ratios, hierarchical cluster analysis (HCA) and principal components analysis (PCA). The net and annual fluxes of PAHs were calculated after a lagoon-wide water sampling campaign and compared with those found in a previous study (Fang, 2007) in which data from only one water sampling station was used. ¡@¡@In rain season, total PAH concentrations ranged from 21.6 to 36.2 ng/L for water samples, with dissolved and particulate phase concentrations ranged from 15.5 to 27.2 ng/L and from 3.4 to 8.6 ng/L, respectively. In dry season, total PAH concentrations ranged from 13.2 to 31.5 ng/L for water samples, with dissolved and particulate phase concentrations ranged from 8.0 to 21.1 ng/L and from 5.3 to 10.5 ng/L, respectively. Total PAH concentrations were found higher in rain season than in dry season. The highest total PAH concentration in dry season was observed in Chianjen River estuary. Relatively high PAH concentrations were also observed in these southern stations of Kaohsiung Harbor because of their location near Dalin industrial park. Total PAH concentrations ranged from 81.7 to 2279 ng/g for sediment samples, with average of 895 ng/g. The correlations between PAH concentrations and organic carbons, water temperature, salinity and suspended particles were also examined in this study. PAH concentration in dissolved phase was negatively correlated with water temperature (p<0.05). PAH concentration in sediment was positively correlated with organic carbons (p<0.05), and negatively correlated with median diameter (p<0.01). The logKoc¡ÐlogKow relationship in rain and dry season was compared with literature. It was found that the logKoc values were higher than those reported in literature, suggesting that soot particles might play an important role in the transport and distribution of PAHs in the study area. In rain season, PAHs in dissolved phase were mainly from pyrogenic origins; while mainly from petrogenic origins in particulate phase. In contrast, in dry season, PAHs in dissolved phase were mainly from petrogenic origins; while mainly from pyrogenic origins in particulate phase. In addition, it was found, relatively, that petrogenic pollution was introduced maily from the northern area of the lagoon. In rain season, total PCB concentrations ranged from 1.1 to 2.7 ng/L for water samples, with dissolved and particulate phase concentrations ranged from 0.42 to 2.1 ng/L and from 0.24 to 1.4 ng/L, respectively. In dry season, total PCB concentrations ranged from 0.54 to 1.3 ng/L for water samples, with dissolved and particulate phase concentrations ranged from 0.20 to 0.74 ng/L and from 0.32 to 0.76 ng/L, respectively. The direction of net fluxes of PAHs in this study are from water to air (net volatilization) in summer. In winter, however, the absorptive PAH fluxes obtained for four to six-ring PAH, such as fluoranthrene, chrysene + triphenylene and benzo[a]anthracene, indicating that PAHs were absorbed into surface waters. According to our results, it was suggested that the results from previous study (Fang, 2007) might underestimate the net fluxes of Pyrene and total fluxes in dry season. The annual fluxes of PAHs estimated in this study were 212 mg/m2 /year and 5.7 kg of PAHs were emitted annually from the harbor lagoon surface waters to the ambient atmosphere.