The T in water is called a flapped T.
For Americans and Canadians, T is sometimes pronounced as an aspirated T [tʰ], unaspirated T [t], unreleased T [t̚], or a short, soft d-like flapped T [ɾ]. The flapped T is not a [d], although to non-native speakers, it sounds like [d].
Rachel's English provides excellent pronunciation videos on youtube. She has a phonetics background and gives accurate information.
Here is one of her flapped T videos.
I find that she overpronounces the flapped T as a full [d]. This may be deliberate to demonstrate.
And here is more information about the several allophones of /t/.