Water behind the filler flap will be the drain pipe getting blocked - poke a bit of coat hanger wire or similar down the hole to clean it out and the water should run out underneath the car.
Water In Diesel Fuel means there is water in the fuel filter (maybe because your filler cap is underwater!) so this needs changing before it gets through to the injection system and screws things up expensively. It could also be that the wrong type of filter has been used and the water sensor in it is giving the wrong signal - same solution though, change the filter.
Have a look at the West Midlands section for some local Alfa specialist recommendations if you need some professional assistance.
"Diesel - Green Fuel of the Future" - Lucas Diesel Systems slogan circa 1992