It now is widely recognised that the global temperature is rising, a phenomenon which could alter the effects of pollution on wildlife. In order to assess the role of temperature and exposure to chlorine due to cooling water discharges, a battery of metabolic, oxidative stress and histological parameters were evaluated in Mytilus galloprovincialis after 15 and 30 days at 15 °C and at two increased temperatures (+5 and +10 °C). Diverse gill pathologies such as haemolymphatic sinus dilatation, an increased number of mucocytes and granulocytes as well as a lower number of cilia were observed after 30 days exposure at higher temperatures. Protein, amino acid, triglyceride and fatty acid levels decreased when the temperature increased, as a consequence of higher energetic demand. Similarly, acetylcholinesterase, catalase and glutathione S-transferase activities showed an inhibition at higher temperatures, although gill lipid peroxidation levels remained unaffected. Our results suggest that increased temperatures induce deterioration in the health status of the mussels and in their defensive capacity against a polluted environment.