If Jesus did walk on water, then we rid ourselves of one problem – the questioning of the historical accuracy of the Biblical account. But we create another - a Christ who only pretended to be human. Because humans can’t walk on water. We can of course protest that Jesus is the Son of God and can do anything, but the moment we do that we open up a whole other set of problems around why Jesus does not do a whole heap of other things that might be felt more useful, like ending wars or saving children’s lives. If we do not want to turn the human Jesus into a capricious divine figure masquerading as a human being, we might have to accept that he did not in fact walk on water.
So, what about this story then? How are we to read it? Well some scholars resolve the problem quite neatly by declaring it to be a misplaced resurrection story. This makes a lot of sense. This is why the disciples for examples are afraid and think they are seeing a ghost. However, I do not think that is the whole answer...