Yes, usually castles are built in high places, but not always.  There are actually a surprising number of castles around the world (and in the UK) built right down on the water.  I'm not sure weather or not the books actually describe Hogwarts high up over the lake or if that's just something the movie did (maybe you can give me a quotation from the books) but I've always imagined Hogwarts lower down set on sprawling lawns leading down to the lake and forbidden forest, not up on this mountain face like the movies show it.  In any case, have you considdered a flood caused by magic?  A magical flood could get deep.  But the reader doesn't yet know what caused the flood (though I do) and it would explain how a castle, even one up on a cliff, could come to be under water.  But as far as the characters in the story know, it very well could be a flood of biblical proportions, they don't know how far it stretches, if it's local or if it goes all the way to the Ministry in London.

Thanks for your review.