The contamination of the marine environment by organic pollutants is a matter of great concern. Bizerte Lagoon is the second largest lagoon in Tunisia, and is known for different industry and fishing activities. The objective of this work is to investigate the distribution of seven polychlorinated biphenyls (PCBs) and nine organochlorine (OCPs) pesticides in water samples collected from the Lagoon of Bizerte. Extraction of water samples was performed by liquid–liquid extraction with hexane. Gas chromatography with 63Ni electron capture detector was used to perform qualitative and quantitative determinations. The average concentrations of OCPs were 0.42 and 14.92 ng L−1. For PCBs the concentrations range between 3 and 10.4 ng L−1. The predominant PCB congeners in the surface water were PCB 28 (0.2–1.4 ng L−1) and PCB 52 (0.8–3.5 ng L−1). The most widespread OCPs were DDTs with a concentration varied between ND and 8.51 ng L−1, heptachlor (ND and 7.83 ng L−1), and endrin (ND and 1.51 ng L−1). These concentrations are generally similar to the background levels from the Mediterranean Sea.