Contamination of fuel storage tanks and delivery systems is the main source of water in the fuel tanks of large transport aircraft.
Fuel quantity indication system defects are often caused by contamination of the fuel. I would always start trouble-shooting by taking a drain sample and checking it for water contamination. In the most extreme case I ever experienced, after refuelling an RAF VC10 there was a discrepancy of about 5,000 pounds between the bowser uplift and the aircraft gauges. I asked the refueller if they had done a drain check after refuelling and he said it was "clear and sweet" I double checked and it was indeed clear. An S.G. check on the sample however, showed an S.G. above point 95 - it was clear water, and almost drinkable! We drained two 40 gallon drums out of one inboard tank before getting a clear, clean fuel sample. I very much doubt if that nearly 80 Gallons of water came from condensation on the tank walls.