Antibiotic contamination is an emerging threat in marine environments due to its potential to alter key physiological processes in non-target organisms. Among veterinary antibiotics, enrofloxacin (ENR), a widely used fluoroquinolone, is frequently detected in coastal waters. This study investigated the biological effects of ENR exposure in the Mediterranean mussel Mytilus galloprovincialis using an integrated approach combining gene expression, biochemical, and bioenergetic endpoints. Mussels were exposed to two environmentally relevant concentrations of ENR (5 and 500 ng/L) for 7 days (EXP7) and 14 days (EXP14), followed by a 14-day recovery period (REC). Gill tissues were analyzed for transcriptional changes in genes related to detoxification, oxidative stress, apoptosis, and energy metabolism. In addition, energy reserves, mitochondrial activity, and indicators of genotoxicity and antioxidant responses were measured. Results showed that ENR exposure modulated the expression of several genes, including early upregulation of abcb and cyp4y1, and downregulation of pkpyr and icdh, indicating activation of detoxification pathways and energy metabolism shifts. Biochemical analyses revealed increased mitochondrial activity (ETS), mobilization of energy reserves, and sustained elevation of GST activity, while DNA strand break levels confirmed a potential genotoxic effect. Despite the removal of the contaminant, most stress responses did not fully revert during recovery. These findings demonstrate that even low concentrations of ENR can disrupt mussel physiology at multiple levels, with effects persisting beyond exposure. The study underscores the importance of incorporating sub-lethal biomarkers into environmental risk assessments and supports the inclusion of veterinary antibiotics like ENR in marine monitoring programs to protect coastal ecosystem health.