Normally there's a small plastic drain screw on the bottom of the filter housing to deal with just this problem-it's common on modern HDi type diesels to have the little warning light, when it stays on you contort your wrist to the base of the fuel filter and undo the drain valve, and simply drain the filter down - there should be a clear plastic pipe there if it hasn't fallen off.
Bosch/PSA filter housings have had had the drain valve for years- it's part of the normal service schedule to drain any water off but its only recently though that they've bothered with having a warning lamp- just something else to get paranoid about I suppose, and if it's not on, then the servicing garage doesn't need to open the drain.
It may be worth making sure the filler neck isn't leaking rainwater into the tank though, or it could have been diesel from a none too watertight garage pump or tank.....