Persistent organic pollutants (POPs) such as polycyclic aromatic hydrocarbons (PAHs) are of great concern due to their persistence, bioaccumulation and toxic effects. In this study, water samples were collected during 2007–2008 from two catchment areas that represent two different models of the aquatic environment in Egypt (Rosetta branch as fresh water and El-Moheet drain as untreated/treated waste water). The distribution of 16 PAHs included in the US Environmental Protection Agency's (EPA) priority pollutant list was analyzed by gas chromatography/mass spectrometry (GC/MS). Total PAH concentrations varied from 242 to 732 ng/L in fresh water from the Rosetta branch with a mean value of 408 ng/L; and for waste water the concentrations were in the range 894 to 1979 ng/L with a mean value of 1476 ng/L. The PAH profiles were dominated by low molecular weight PAHs (two- and three-ring components) in all collected water samples. The origin of PAHs in both waste water and fresh water in these study areas may be from oil or sewage contamination. The total PAHs concentrations of untreated waste water decreased along the treatment process by about 30% at the Zenein waste water treatment plant. The levels of PAHs in waste water are relatively high, although lower than locations with known problems.