Some observations on the B777 fuel system
The centre tank is a large relatively flat based structure. The centre tank pump inlets are uncovered at about 900kg fuel remaining. The centre tank water scavenge pumps are always running, scavenging liquid from the bottom corners of the tank and delivering it to the booster pump inlets. The centre tank transfer jet pumps are running all the time, but will not deliver fuel to the wing tanks until they have dropped substantially (I posted the figures here a few days ago). There are also water scavenge pumps in the wing tanks that are always running.
Jet pumps have no moving parts. They take motive power from the booster pump outlets and direct it through a nozzle that creates a low pressure and sucks liquid up from the collector pipes. Typically a pump will have about 8 inlet pipes. These pipes are very small, say quarter of an inch dia. I have never been inside a B777 tank, but have good memories of working on Tristar scavenge systems which are very similar. The volume of liquid moved is very small and if all the jet pumps were sucking pure water it would never be enough to affect the flow of fuel to the engines.
Very occasionally an aircraft will land with fuel remaining in the centre tank. This will be because the jet pumps are blocked with debris. Small pieces of tank sealant will clog the nozzles. These are checked on major checks when the tanks are opened up.
Because of the flat bottom of the centre tank, there must be a lot of water in there (138 gallons) before the water sensing system could see it. It is spread over a large surface area. It is the same reason why the centre bank booster pumps stop pumping so early.
Water in tanks does not come from the fuel supplied. In my career I have done thousands of fuel water checks on bowsers, and never had a positive reading. The water comes from moist air that is present in the tanks when they are empty, the moisture condenses on the walls and drops into the bottom of the tank. We sump the tanks regularly to remove this water. Usually a few drops at most comes out of each tank. The reason for so little water is that the water scavenge systems work.
You cannot sump the tanks on the ramp during refuelling. It takes a long time for the water to separate out and accumulate on the bottom of the tank. It is done on layover checks every couple of days.