Polycyclic aromatic hydrocarbons (PAHs) in surface microlayer (SML) and subsurface water (SSW) of Lagos Lagoon were investigated using gas chromatography-electron capture detector (GC-ECD) technique to ascertain their occurrence and spatial distribution, origin, enrichment, and carcinogenicity. Total PAH (ΣPAH) concentrations ranged from 9.10 to 16.20 μg L(-1) in the SML and 8.90 to 13.30 μg L(-1) in the SSW. ΣPAH concentrations were relatively higher in the SML than the underlying SSW samples. The enrichment factors (EFs) of ΣPAHs ranged from 0.76 to 1.74 while the EFs of the individual PAHs varied from 0.50 to 2.09. In general, the EFs values calculated in this study were consistent or slightly less than the EFs reported for similar coastal seawater ecosystems. A correlation between the EFs of fluoranthene and pyrene indicated a positive significant value (R = 0.9828, p < 0.0001, n = 6). Source analyses using the phenanthrene/anthracene and fluoranthene/pyrene ratios indicated the dominance of petrogenic-derived PAHs. Furthermore, enhanced concentrations of BaP (strong carcinogenicity) in SML and SSW samples, which resulted in higher EFs, could pose serious ecological and human health risks.