If you are the thing flying, you can not fly over water. Vampire can not actively move over water, it's sort of like how they can't enter private buildings. Something could carry you over water if it could fly, but the vampire would be helpless like that. Unless the thing flying was some sort of solid object between the vampire and water. To get on the ship you would need to fly over top the gangplank, and once above the ship you could only fly where there is ship under you.<br/><br/>The monster manual states that a vampire loses 1/3 of it's hit points each round in the water, on the third round it's destroyed. It's doesn't say but from the way I read it it looks like it's remaining hit points. so if you had 3 hit points left you would lose one each round and then die on the third.