The spatial distribution of water molecules and their corresponding hydrogen-bonded network inside bacteriorhodpsin (bR) in its ground state conformation were investigated by molecular dy-namics simulation. The protein was embedded in a fully hydrated lipid bilayer membrane. A much higher average number of internal water molecules (44) than observed in crystal structures (18) was found in our simulation. This discrepancy is due to the high mobility of these water molecules between different positions. The simulations provides new and valubale insights into the structure and lifefetime of water-mediated hydrogen-bonded networks used for proton translocation during the photocyle of bR.