Background, aim, and scope In this study, a suite of sublethal stress biomarkers were analysed in juveniles of the sentinel species, the Pacific oyster Crassostrea gigas, with a view to using them as pollution monitoring tools. The aim of this work was (1) to study baseline seasonal variations of biomarkers in different body compartments of C. gigas in the reference site and, after selecting biomarkers presenting no seasonal variations, (2) to compare responses of these biomarkers between contaminated and reference sites. Materials and methods Juvenile oysters were transplanted from Bouin (France), a reference site, to three different sites in Marennes-Oleron Bay (France), located in another water body and next to different contamination sources. Animals were exposed in situ for 3 months in summer, autumn and winter. The following biomarkers were measured: superoxide dismutase (SOD) and glutathione peroxidase (GPx) in gills and digestive gland, and lysozyme and phenoloxidase (PO) in plasma. Results No significant seasonal variations for SOD in gills and digestive gland, GPx in gills, and PO in plasma were observed in the reference site. Significant differences in enzyme activity were observed between contaminated and reference sites for SOD in gills and digestive gland, and PO in plasma, depending on the body compartment, the season and/or the site. Conclusions In conclusion, these data suggest the potential application of these biomarkers in C. gigas to provide ecologically relevant information and therefore, to be used as biomarkers in coastal pollution monitoring.