The aim of the present study was to investigate the combined effects of seasonality and anthropogenic pressure on a battery of oxidative stress, lipid peroxidation, protein oxidation, DNA damage and histological alterations in the native clam Ruditapes decussatus collected from a less contaminated area (LCA), Ghar El Melh, a moderately contaminated area (MCA), the North Lake, and a highly contaminated area (HCA), the South Lake, all located in the southern Mediterranean Sea. The accumulation of cadmium, lead, copper, iron and zinc was higher in the digestive glandsof clams collected from the MCA and the HCAthan in those from the LCA, particularly during the warm season. Our results reveal that metallothionein, lipid peroxidation, protein oxidation levels and antioxidant defence systems were higher, while acetylcholinesterase activity was lower, in clams from the MCAand HCAthan in those from the LCA. The results also indicate that clams from the MCA and the HCAare characterized by histological alterations and DNA damage. In conclusion, the evident changes of antioxidant defence systems and macromolecules between the studied lagoons reveal the perturbation of the physiological states of clams from polluted sites thatcope with seasonal changes and trace element accumulations.