This study aimed to understand bivalves’ (Scrobicularia plana) adaptive strategies, with emphasis on mitochondria as a target organelle, in response to mercury-contaminated environment. Inter-age and organ-specific approaches were applied using different annual size classes (2+, 3+, 4+ and 5+ years old) and assessing specific organs (gill, digestive gland), respectively. Bivalves were collected from moderately (M) and highly (H) contaminated sites at Laranjo basin - Ria de Aveiro (Portugal), where a mercury gradient was identified, and compared with those from a reference (R) site. Total antioxidants capacity (TAC) was measured in mitochondria, whereas the lipid peroxidation was assessed as a marker of damage. S. plana age determined the clams’ vulnerability towards mercury induced mitochondrial peroxidative damage depending upon the mercury accumulation: younger animals were more vulnerable than older. Clams showed a decreasing trend of TAC with increasing age. This decrease was found to be statistically significant in 4+ and 5+ years at M; whereas, at H, with depleted TAC, remained same until they have grown 5+ years. The organ specificity was evident for antioxidant response and peroxidative damage. A clear pattern of overall TAC increase in digestive gland (at M) and decrease in gill (at H) was observed, while only gills were found to be susceptible to peroxidative damage. Overall, mitochondria proved to be a sensitive fraction for the effects of mercury in S. plana inhabiting mercury contaminated area.