There is a little published information on pattern of Polycyclic aromatic hydrocarbons (PAHs) pollution on marine protected areas. 36 sacrificial sediment samples were collected from four stations in Siah-Kashim Lagoon on a temperate season (autumn). The samples were frozen and transported to laboratory and kept in -35 freezer till analysis. 16 Environmental Protection Agency (EPA) priority PAHs were extracted, cleaned up and quantified by fluorescence detector in a high performance liquid chromatography (HPLC) apparatus. An aliquot of the samples were also treated for total organic matter (TOC) determination. The results showed that within low level of pollution with respect to PAHs in the studied area, the concentration (i.e. availability and environmental toxicity) of PAHs in Siahkashim Lagoon is governed first by their water solubility and then their Octanol-Water partition coefficient (Kow).