Transitional waterbodies, such as estuaries, are highly diversified environments with respect to ecology, geophysics, and nature of anthropogenic impacts. This spatial heterogeneity may pose important constraints when developing monitoring programmes for aquatic pollution. The present study compared three distinct coastal ecosystems located in Southern Portugal (subjected to different anthropogenic stressors), namely, two estuaries and a coastal lagoon, through the characterisation of sediment contamination and a biomarker approach to an important commercial clam (Ruditapes decussatus) obtained from local fishing grounds. The results showed high heterogeneity of sediment contamination for both estuaries and a marked distinction between industrially and agriculturally influenced areas as well as between natural and artificialized sites. Hydrodynamics and oceanic influence (in essence dictating sediment type) play a major role in environmental quality. Environmental heterogeneity constituted an important confounding factor for biomarker analysis in the clams' digestive glands since the animals appeared to respond to their immediate surroundings' characteristics rather than the geographical area where they were collected from, despite the relative distance to pollution hot spots. Still, oxidative stress biomarkers (lipid peroxidation and catalase activity) could correlate with each other and to both organic and metallic contamination, whereas metallothionein-like protein induction failed to correlate to any class of sediment toxicants (albeit metals being the most representative pollutants) and appeared to be strongly affected (unlike the previous) by clam size and probably other unknown internal and external variables, among which contaminant interactions should play a major role.