In previous work  we showed that the CO-bridging configuration had to be stable for the [FeFe]H cluster of hydrogenase to function as an efficient hydrogen-production catalyst. We found that in vacuo, however, the CO-terminal configuration was slightly more stable and would effectively stop catalytic action. In practice, the catalyst would be linked to the surface of an electrode of the surface of a photovoltaic device and immersed in water. Accordingly, we have investigated by first principles molecular dynamics simulations the effects of a water environment on the structure, stability, and activity of the cluster with a candidate linking moiety. We found a remarkable competition for protons among the five plausible protonation sites of the [FeFe]H cluster in its various charge states. The most significant effect found is the stabilization of the bridging configuration by water molecules weakly hydrogen bonded to the protonated distal CN ligand. This finding supports the interpretation of the stability of the bridging configuration in the enzyme as due to hydrogen bonding of the distal CN to a cysteine residue in the protein backbone. Consequences for the H2 production cycle and link stability will be discussed as well.