Al-Arbaeen and Al-Shabab are two highly polluted lagoons lying along the Jeddah Coast. Surface sediments were collected from both lagoons to assess the levels and spatial distribution of polycyclic aromatic hydrocarbons (PAHs), as well as study the effect of environmental conditions on PAH concentrations. The concentration ranges for Σ38-PAHs in Al-Arbaeen and Al-Shabab lagoons were 5.4-5,372 ng/g (mean 1,637 ng/g) and 60-7,927 ng/g (mean 1,323 ng/g), respectively. Pollution levels in both lagoons were in the low-very high range with dominance by three- and four-ring congeners. Pyrene was the dominant congener, while benzo (a) pyrene represented the dominant carcinogenic congener in the study area. The disappearance of most of the low molecular weight congeners may be attributed to temperature and microbial activity. Carcinogenic PAHs contributed 59.9 and 23.6% for Al-Arbaeen and Al-Shabab lagoons, respectively. The diagnostic ratios revealed that the source of PAHs are of mixed origin and site specific. The probable toxic effects on organisms were examined for total and individual PAHs with sediment quality guidelines (ERL-ERM). The detected PAHs levels in the present study were compared with reported levels for coastal worldwide lagoons.