The molecular dynamics simulation is reported. The latest data on photosystem II structure, a thylakoid membrane model with the same lipid class distribution and fatty acid composition as the native thylakoid membrane, are used. The results indicate that the transfer of water, oxygen and protons has different pathways. The root mean square (rms)-fluctuation analysis of trajectory revealed that the residues surrounding the oxygen-evolving center (OEC) show small fluctuations and that most of the water molecules there show large fluctuation and are on proposed pathways for water and oxygen transfer. The water molecules near the OEC having small fluctuation could be involved in proton transfer. We assume that each kind of pathway characterized in this study plays a role in photosynthesis.