The only thing that walks on water on two legs is a south American lizard; and it sure isn't a messiah!
If you consider quantum mechanics, it becomes possible as I understand it. If you can manipulate the wave function of the water in question, (or the wave function of Jesus) then walking on water should be a piece of cake.
If you consider string theory, it also should be possible. After all, if you somehow manage to manipulate the vibrations of the strings you can change any particle into any other particle.
Of course this requires the ability to manipulate certain things that are very hard to manipulate, but I am not aware of it being impossible to do as I just suggested. Furthermore, if you consider God a being who is above/beyond our current physical frame of reference (the three dimensions of space and one of time) it is very far from impossible that He could manipulate anything within our three dimensions in manners that to us seem miraculous without He Himself being observed directly. I don't know that this would violate any physical laws either. Supposing God can move about at will in higher dimensions it should not be hard for Him to hold Jesus at a position where He would not sink into the water.
Given the speculation some physicists make that gravity is a force which is capable of leaking into other parallel universes another possible solution would be a highly focused beam of gravitons emitted from another universe could simply warp space (as gravity does) to pull Him in another direction than earth's own gravity field does.
Do I consider walking on water to be impossible? No. I don't. It's not something we can do at this point, true. But I don't think it's impossible.
We could conceivably alter the nature of the water. We could alter Jesus' physical properties or warp space around Him.
After all:
Any sufficiently advanced technology is indistinguishable from magic. Arthur C. Clarke
It's not long ago we considered the atomic theory nonsensical. Today we even have quantum mechanics and M-theory. Both quite counter intuitive.
There's much we don't know. Dismissing this seems to me as a somewhat premature conclusion. I don't see it being completely impossible if we factor in a powerful extra/super/multi dimensional being like God into the equation. It could be accomplished without breaking the laws of physics at all. Though from a newtonian single-universe three-dimensional earth-centric viewpoint it certainly would seem utterly impossible.