Note that the game will not switch from an empty waterskin to a full one for you (which is what it sounds like you were expecting). Each waterskin is filled and consumed separately.
To fill them, add them all to your hotbar, then use each of them at a water source until they all show a full bar. Afterwards, you can return them to your character’s inventory.
To use them, you can either keep one on a hotkey slot and use it until empty, or open you inventory, select one and the press the Use key on it.
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