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The concentrations of 16 polycyclic aromatic hydrocarbons (PAHs) in surface water samples collected from three locations along the downstream of river Nile in Alexandria, Egypt were analyzed using gas chromatography–mass spectrometry. To the best of knowledge, this investigation represents one of the very few extensive studies investigating the distribution and sources of PAHs in water of river Nile in Egypt. Total concentrations of the 16 PAHs in water samples ranged from 235.92 ng L−1 at Abbis site (an agricultural area), which were predominated by three- and four-ring PAHs (about 90%) to 10367.60 ng L−1 at Al-Max area (a residential area with heavy traffic and fishing activities), which were predominated by five- to six-ring PAHs (about 94%). PAH concentrations were one to two orders of magnitude higher in comparison with those reported for riverine/estuaries systems around the world. Molecular indices, such as ratios of specific PAH compound including Phenanthrene/Anthracene (Phe/Ant) and Fluoranthene/Pyrene (Flua/Pyr), were calculated to evaluate the possible sources of PAHs and their relative importance. These ratios indicated that the major PAH input was from combustion of fuel, wood and grasses in the area under study (i.e. a pyrogenic source). The concentrations recorded in this investigation were higher than that recorded in the rivers of the USA and Europe and even higher than the levels established for drinking water in the USA. [ABSTRACT FROM AUTHOR]