In reply to MG:
More conjecture, but I don't think you'd get a big flash and flames like a transformer. It's only 600V, so if there was a sudden surge of water covering a length of track I think it would blow the fuse without too much to see. If the water rose gradually until it flashed over at a point, I think it would boil at the point and this would quickly spread along the rail as the steam made it conduct across the gap. No big sparks, but there's quite a bit of energy require to blow the fuse, so you wouldn't want to be standing next to it.
I assume the rail companies have sensors to kill the power in any likely flood points though...