The Western Mediterranean coast is under the influence of anthropogenic pressures, including land use, increasing amounts of dangerous waste and habitat destruction. In 2021, the French RINBIO network (http://www.ifremer.fr/envlit/) originally dedicated to assess chemical contamination in the region, focused on biological effects produced by contaminants and the interaction with natural variability in mussels using an active caging strategy. Cell and tissue level biomarkers were applied for 17 sampling sites divided in three sub-regions categorized by different environmental conditions. Results provide critical information for ecosystem health assessment using mussels as sentinel species in the Western Mediterranean Sea. The influence of natural and confounding factors (trophic condition, reproductive cycle, caging strategy), on biological responses to mild chemical contamination, was discussed and discriminated for health status assessment. Results provide valuable data available as reference values for the assessment of biomarkers and histopathological alterations for large-scale active biomonitoring campaigns in the Western Mediterranean Sea.