Microalgae are aquatic organisms possessing molecular mechanisms that allow them to discriminate non-essential heavy metals from those essential ones for their growth. The different detoxification processes executed by algae are reviewed with special emphasis on those involving the peptides metallothioneins, mainly the post transcriptionally synthesized class III metallothioneins or phytochelatins. Also, the features that make microalgae suitable organisms technologies specially to treat water that is heavily polluted with metals is discussed.