Let's insert a miracle at the point where a fairly substantial amount of water becomes wine in a very short period of time. What, scientifically speaking, is "supernatural" about such an occurence? Oh. It doesn't happen every day? Neither does a nuclear explosion. Neither does your birth into this world.
In the case of this well-attested "miracle" it starts as a liquid and ends as a liquid. The chemical makeup of water and wine, on a percentage basis, is how much different one from the other? Not much different. If you were the one who designed and manufactured H2O how much trouble would it be to tweak it on a special occasion just to point something out? Not much trouble, but very much worth it, especially if one's life were at stake.
None of the things related by the biblical texts and reported as "miracles" are so preposterous as to throw into doubt physical reality, scientific certitude, or the "course of nature." The supernatural nature of reality comes into play when thought comes into play. Here we are dealing with more than flesh and blood. Here we are dealing with principlities and powers which, while not currently under the purview of general science, are no less real than the screens before our eyes.
Actually wine has elements that water does not have, so in order water to turn into wine you'd need 1)devine power or 2)a combination of fission or fusion of the H and O atoms.