At a previous employer (bakery), we had the water dispensers (or a water cooler that was filled by the supervisor) on the floor with the cone, disposable, paper cups. It was kept away from the production lines and employee's were not permitted to carry the disposable cup to their work station. It was also on a cleaning schedule, and only the supervisors could fill it up to ensure that only water was ever put in it. In the warehouse area, water bottles were permitted at one job location where the employee couldn't leave their work area. They were only permitted to have a clear bottle that had a cap that was connected to the bottle - as we didn't want caps to get lost. Product was already in a sealed package by this point.
At a different employer (coffee production), water dispensers were at each line, with cone shaped cups that were disposable. In the roasting area (which was a control room), operator's were allowed to have water - whether in a cup, bottle, etc. - at their work station (desk/computer). They were not permitted to take it out to the roasters themselves.
At my current job (another bakery), we do not let any sort of water bottles on the production floor, but we do have water fountains.
I would include whatever you decide on in a policy - possibly your GMP's - as well as train on it so that employee's will know what they are allowed to do/not do. At the end of the day you need to take your operator's safety into account as well as the safety of the product.