The impact of industrial, rural, and urban activities on two runnels (B1, B2, and B3 from Beausset runnel and V1 and V2 from Vallat du Ceinturon runnel) located in the Palun marshes (Berre lagoon, France) was evaluated by analyzing 16 polycyclic aromatic hydrocarbons (PAHs), 1-nitropyrene (1-NP), 1-aminopyrene (1-AP), and six pesticides in sediment samples. The mutagenicity was assessed with the Salmonella mutagenicity test using tester strains TA98+S9 Mix and YG1041 +/- S9 Mix. The clastogenicity was evaluated with the micronucleus assay on Chinese Ovarian cells +/- S9 Mix. A gradient of PAHs concentrations was observed from B1 (3359 microg kg(-1) dry weight [dw]), close to industrial zones, to V2 (497 microg kg(-1) dw), away from the source of pollution. Similar gradient was noted for 1-AP (from B1: 11.8 microg kg(-1) dw to V2: 0.6 microg kg(-1) dw). However, this trend was not observed in 1-NP concentrations (concentrations ranged from 1.2 microg kg(-1) dw [V1] to 0.4 microg kg(-1) dw [B1]). Pesticides were detected in all samples. Diazinon and dieldrin were found in high concentrations in B1 extracts (74.5 and 39.9 microg.kg(-1) dw, respectively). All the sediments except V2 were mutagenic with strain TA98+S9 Mix. The mutagenicity was linked to the presence of PAHs (V1), nitroarenes (B1 and B3) and aromatic amines (B2). All sediments were clastogenic with and without S9 Mix except V1 extract, which was negative without S9 Mix. Overall, the two runnels in the Palun marshes were found to be polluted by many organic compounds that originate from direct human activities and pose a significant genotoxic risk.