Various kinds of roles of the water molecules in the electronic states of the complexes of metal ions (M) and deoxyribonucleic acid (DNA) are reviewed. Divalent metal ions M like Fe, Mn, Zn and so on, form Metal-DNA complexes (M-DNA) with each metal ion between the bases of a base pair of DNA. The electronic states of the complexes depend on the species of ions in M-DNA. Metal ions in Fe-DNA and Mn-DNA possess 3d magnetic moments, but those in Zn-DNA do not. Interestingly, the magnetic property of the complexes, especially the magnetic interaction between the metal ions, is dominated by water molecules in the complexes. In Fe-DNA, the water molecules play a role of ligands for the iron ions, which controls the spin states of Fe3+, whereas they govern the magnetic interaction between the Mn2+ ions in Mn-DNA. In contrast, Zn-DNA has no 3d magnetic moment, but the water molecules dominate the bonding states of the Zn ions and the magnetic states of the Zn-DNA system.