Aquatic wildlife is exposed through trophic transfer of hazardous substances to several threats inducing physiological impairments. We aimed at assessing the impact of contamination in one of the hot spots of pollution along Mediterranean coasts, the gulf of Gabes in Tunisia, on Common tern Sterna hirundo, a piscivorous top predator bird. Firstly, we compared the reproductive effort of breeding adults through clutch size distribution in three sites with different levels of pollution. Then, a battery of genotoxicity and oxidative stress biomarkers was carried out to assess physiological impairments in chicks. While defense mechanisms showed a depletion, lipid peroxidation and genotoxicity increased significantly according to pollution level. The multi-biomarker approach used here, discriminated chicks according to contamination degree of their nesting sites. Increases in genotoxicity and oxidative stress were correlated to a decrease in chick body mass known to lead to long-term impacts on juvenile survival and recruitment in birds.