Biomarkers involved in detoxification process (GST), oxidative stress (SOD and MDA), immune response (Laccase) and neurotoxic disorders (AChE) were analysed in Pacific oysters and blue mussels collected from 4 locations within the Pertuis sea (France). Seasonal variations of total pesticide mean concentrations were found in seawater with metolachlor being the main pesticide measured (up to 32 ng/L). The majority of pesticide concentrations in sediment were below the LOD. Seasonal contamination differences were evidenced for chlortoluron, especially in mussels where concentrations reached 16 ng/g (wet weight) during the winter, in the Charente estuary, but no relationships with any of the biomarkers selected arisen. Actually, low concentrations of alpha-, beta-BHC and alachlor were correlated to GST activity, and low levels of hexachlorobenzene were linked to the AChE activity and MDA content in oysters. In mussels, low concentrations of methylparathion, parathion and beta-BHC were correlated to laccase. •The concentrations of 30 pesticides in biota, sediments and seawater were relatively low.•Seasonal variations of chlortoluron concentrations were found in mussels.•Metolachlor was the main pesticide measured in seawater.•The majority of pesticides in sediments were below the limit of detection.•Environmental factors were correlated to biomarker responses.