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Urban and hospital-sourced pharmaceuticals are continuously discharged into aquatic environments, threatening biota. To date, their impact as single compounds has been widely investigated, whereas few information exists on their effects as mixtures. We assessed the time-dependent biological impact induced by environmental concentrations of caffeine alone (CAF; 5 ng/L to 10 µg/L) and its combination with salicylic acid (CAF+SA; 5 ng/L+0.05 µg/L to 10 µg/L+100 µg/L) on gills of mussel Mytilus galloprovincialis during a 12-day exposure. Although no histological alteration was observed in mussel gills, haemocyte infiltration was noticed at T12 following CAF+SA exposure, as confirmed by flow cytometry with increased hyalinocytes. Both the treatments induced lipid peroxidation and cholinergic neurotoxicity, which the antioxidant system was unable to counteract. We have highlighted the biological risks posed by pharmaceuticals on biota under environmental scenarios, contributing to the enhancement of ecopharmacovigilance programmes and amelioration of the efficacy of wastewater treatment plants.