El Bey river, which drains 60% of the pollutant load of several urban cities in the northeast of Tunisia, provides a good example of the transfer of organic and metallic pollutants that result from industrial and urban activity, and can be used to show how these charges are transported and discharged into the Gulf of Tunis. Persistent organic pollutants (PAH and PCB) in dissolved, particulate matter, bed sediments, and three wastewater effluents in El Bey watershed were analyzed. PAH (∑14PAHs) concentration ranged from 0.248 to 9.955 mg L−1 and from 0.836 to 28.539 mg L−1 in dissolved and particulate fraction respectively. The particulate/dissolved partition coefficient value (Kd) was less than one which confirmed the affinity of PAH to be adsorbed. In sediment, the high-molecular weight PAHs were found principally with percentage between 50 and 100% witch present 239.99 to 5362.19 μg kg−1, which is relatively higher in comparison with other estuaries river. Contrary to PAH patterns, PCB were bound to dissolve fraction. Kd (PCB) value (Kd > 1) reflected this affinity which is related to environment energy. The spatial distribution and profile of analyzed organic pollutants confirmed the direct impact of wastewater effluent on the organic pollution level in three compartment of El Bey watershed and his profiles suggested different transport patterns.