ffb,
Im assuming you are talking about the main fuel tank strainer (under the wings) check in which case the fuel pump has got sod all to do with the checking of the left and right fuel tanks for any water.
There is unlikely to be any water collected between the main tanks and the engine, unless it has been taken from contaminated fuel in the main tanks. The main check to worry about is making sure there isnt any water present in BOTH L and R fuel tanks. Most likely to be found first thing in the morning after sitting all night, or if the aircraft has been parked up for a while.
Hope this helps you!!