Water channels are important if you want to move protons through a protein. The problem is that protons are hydrated, at their simplest they can be thought of as the hydronium ion, H3O+, but it seems more likely that 4-6 water molecules form a structure around this giving a large molecule restricted to channels where there are adequate ionised amino acids to form an hydrophilic environment rich in water molecules.
Nqo8's amino acid then protonates
As the protons exit, the associated conformational changes open the cytosolic water channels and the cycle is ready to repeat
This is all very nice and neat, typos excepted, with four protons pumped per cycle. But there is a fly in the ointment. As the authors comment