Empty water bottles (and other containers) are not on the prohibited items list. Once in a while a TSA executive or spokesman will make that clear in an interview.

The TSA's website does not make that rule clear, however, and there are multiple reports of pax having their empty containers confiscated/stolen by TSA. Personally I've not yet had a problem, and I always have an empty watter bottle in my laptop bag when going through TSA.

Not that prohibiting water makes any sense at all, but prohibiting empty containers would make even less sense since one could purchase a bottle airside and them empty it yourself.