It is the only water that gets charged and not the bottle. Once you have consumed the charged water, fill the bottle with new water and charge again. Charging empty Bottles will not help. You have to charge only water, consume it, refill it, and again consume it.
If you have charged a bottle full of water. You consumed water half or more/ less, and then you filled it with uncharged water, please charge the water again. Freshwater will require charging again. You will obviously charge the water with the same energies, that you did for previous water.