With the aim of studying levels of antioxidant and peroxisomal enzymes and the structure of peroxisomes in relation to body burdens of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), mussels Mytilus galloprovincialis, oysters Crassostrea sp., crabs Carcinus maenas and mullets Mugil cephalus were sampled in two Basque estuaries (Bay of Biscay): Urdaibai (Laida, Txatxarramendi, Arteaga, and downstream a sewage treatment plant-STP) and Plentzia. In general, animals showed higher concentrations of contaminants in winter than in summer and no relevant differences were detected among locations. Conversely, antioxidant enzyme activities were higher in summer. Enzyme expression was studied in mullets using immunochemical methods. By immunoblotting season-dependent differences were detected for Mn-superoxide dismutase (Mn-SOD). As for the immunohistochemical staining, mullets sampled in summer in Plentzia showed significantly higher optical densities for acyl-CoA oxidase and lower for both Cu,Zn-SOD and Mn-SOD than those collected downstream a STP as well as higher catalase immunostaining than those collected in winter. Peroxisomal volume density (V(vp)) of mussels sampled in Laida and Txatxarramendi did not show seasonal variations, while for oysters collected in Laida and Arteaga V(vp) was higher in summer. Crab and mullet V(vp) were also higher in summer. In conclusion, the estuaries of Urdaibai and Plentzia can be considered as low to moderately polluted areas and levels of PAHs and PCBs do not show marked variations apart from seasonal variations. Animals can be adapted to low pollution conditions and, under these circumstances, seasonal factors might affect biomarker responses to a greater extent than pollution variations.