The black chocolate clam Megapitaria squalida is a commercially important bivalve along the Pacific coast of Mexico and is used as a bioindicator in environmental health studies. Previous studies of Bahía de La Paz indicated significant differences in heavy metal content among localities in this clam. To identify areas affected by heavy metal pollution, lipid peroxidation (TBARS) levels and activity of superoxide dismutase (SOD) and glutathione S-transferase (GST) were measured in muscle, gonad, and digestive gland tissue and correlated with heavy metal levels of clams from six localities along the shore of the bay. Significant differences in TBARS levels and antioxidant enzyme activity were found among these tissues at all localities. Such differences are ascribed to the physiology of each organ. Higher levels of TBARS were found in areas with higher cadmium content. SOD activity in muscle correlated positively with cadmium, lead, and iron in areas with a higher content of those elements. This study suggests that TBARS levels and SOD and GST activity are affected by biotic and abiotic factors and have potential as indicators of heavy metal contamination.