Water ligands found in the oxygen-evolving Mn(4)CaO(5)cluster in photosystem II are thought to be important during photosynthesis, but the nature of the proton-releasing substrate water molecules is disputed. Here the pKa values of four key water molecules are estimated, with implications for the mechanism of water oxidation. Release of the protons from the substrate water molecules is prerequisite for O(2)evolution in photosystem II (PSII). Proton-releasing water molecules with low pK(a)values at the catalytic moiety can be the substrate water molecules. In some studies, one of the ligand water molecules, W2, is regarded as OH-. However, the PSII crystal structure shows neither proton acceptor nor proton-transfer pathway for W2, which is not consistent with the assumption of W2 = OH-. Here we report the pK(a)values of the four ligand water molecules, W1 and W2 at Mn4 and W3 and W4 at Ca2+, of the Mn(4)CaO(5)cluster. pK(a)(W1) approximate to pK(a)(W2) << pK(a)(W3) approximate to pK(a)(W4) in the Mn(4)CaO(5)cluster in water. However, pK(a)(W1) approximate to pK(a)(D1-Asp61) << pK(a)(W2) in the PSII protein environment. These results suggest that in PSII, deprotonation of W2 is energetically disfavored as far as W1 exists.