Harbours of La Goulette, Rades and Sidi Bou Said are considered as the principal largest and most important port in the Gulf of Tunis characterised by a direct influence of different activities (sailing, industry and fishing) to the Mediterranean Sea. Due to their social and economic impact, a comprehensive assessment of the spatial distribution and partitioning of 24 polycyclic aromatic hydrocarbons (PAHs) and 18 aliphatic hydrocarbons (AHs) in summer and in winter among overlying water, suspended particulate matter (SPM) and surface sediments is essential. Distribution of hydrophobic organic contaminants in abiotic compartments is important for describing their transfer and fate in aquatic ecosystems and to identify the potential danger due to mobilization of contaminants produced by managing of the same sediments. Total organic carbon (TOC) contents range between 4.3% and 6.5%, with an average value of 5.9% in summer, and between 2.3% and 9.6%, with an average value of 6.1% in winter. The average concentrations of ΣPAH in winter and in summer were respectively 703.1 ng L⁻¹ and 378.4 ng L⁻¹ in seawater, 4599.1 ng g⁻¹ and 3114 ng g⁻¹ in SPM, and 1507.6 ng g⁻¹ dw (dry weight) and 1294.6 ng g⁻¹ dw in surface sediment. For ΣAH the average concentrations in winter and in summer were respectively 701 ng L⁻¹ and 741.7 ng L⁻¹ in seawater, 6743.5 ng g⁻¹ and 6282.9 ng g⁻¹ in SPM, and 4971.3 ng g⁻¹ and 4588.1 ng g⁻¹ in surface sediment. Higher PAH and AH concentrations were observed in SPM than in surface sediment. SPM and water were dominated by PAH with low molecular weight, while for sediment low and high molecular weight PAHs were present. PAH and AH fingerprint ratios, such as pristane to phytane (Pr/Ph), phenanthrene to anthracene (Phe/An) and fluoranthene to pyrene (Fl/Py), suggest that hydrocarbons in all harbours may originate from both pyrolytic and petrogenic sources derived from discharge of untreated sewage and wastewater or from direct input by ship traffic in the area. The results showed significant difference (ANOVA, p < 0.05) for hydrocarbon mean concentrations between all harbours studied and between different matrixes.