The presence of pharmaceuticals in coastal ecosystems represents a crucial issue caused by the massive use and the often limited removal of those compounds from the environment. Pharmaceuticals are ubiquitously present in water column and sediment, and a widespread bioaccumulation in tissues of different aquatic species has been demonstrated with deleterious outcomes in many invertebrate species. The present study aimed to investigate the influence of reduced pH on bioaccumulation, excretion and sub-lethal effects of the pharmaceutical Carbamazepine (CBZ) in the mussel Mytilus galloprovincialis. A multidisciplinary approach was applied integrating measurement of drug bioaccumulation with a large number of biomarkers and transcriptomic analyses to clarify the activation of molecular mechanisms and potentially elucidate the intricate Mode of Action of CBZ in marine mussels.