The marine diatom Skeletonema costatum was used to study mechanisms of detoxification when submitted to cadmium and copper contamination. After 96 h of growth, concentration corresponding to 50% growth inhibition (IC50, 96 h) was 0.224 mg/L for cadmium and 0.045 mg/L for copper, indicating that copper is more toxic for S. costatum than cadmium. Heavy cellular damages were observed for cadmium and copper concentrations close to the IC50. Exposure to these concentrations induced a migration of inclusions from the peripheral cytoplasm to the vacuole. Electron energy loss spectroscopy (EELS) investigations demonstrated that Cd and Cu were specifically trapped in these inclusions. However, Cu was less sequestered than cadmium in the vacuole. EELS determination of oxidation states evidenced that trace metals were sequestered as Cd2+ and Cu2+. Nitrogen and sulfur are involved in metallic storage, especially in the case of cadmium contamination.