La Goulette, Rades and Sidi Bou Said harbours are considered as the most important commercial and tourist ports in the Gulf of Tunis. They are located on the northeast coast of Tunis and receive industrial and municipal wastewaters from Tunis city. The contamination level of copper, lead, zinc, cadmium, manganese, iron, total nitrogen and total organic carbon in the surface sediments was assessed on the basis of the enrichment index factors and corresponding to sediment quality guidelines. The results revealed moderate to highly elevated concentrations near to the sites of intense industrial, shipping and/or commercial activities suggesting a direct influence of these sources. In winter and summer, concentrations varied for cadmium, 0.28–1.40 mg kg−1; lead, 18–217 mg kg−1; zinc, 87–459 mg kg−1; copper, 8–121 mg kg−1; manganese, 208–254 mg kg−1; and for iron, 24–40 g kg−1. Furthermore, in summer the concentration of the total organic carbon and the total nitrogen contents range between 4.3–6.5 % and 0.06–0.49 % with an average value of 5.9 and 0.15 %, respectively. Whereas, in winter, total organic carbon and the total nitrogen concentrations varied between 2.3–9.6 % and 0.03–0.22 % with an average value of 6.1 and 0.14 %, respectively. The levels of lead, copper, zinc and iron in suspended particulate matter content range between 3.1–27.5 mg kg−1; 0.4–11.7 mg kg−1; 1–1.5 mg kg−1; 1.2–1.7 g kg−1, respectively. This study revealed that heavy metals pollution is mainly localized in the commercial (Rades) and fishing (La Goulette) harbours and not in the yachting (Sidi Bou Said) harbour.