There are multiple ways to refill your Sealed Waterskin.
The basic concept of refilling requires you to stand as close as possible to reservoir, river or a well and press the button from the action bar that it is assigned to. The white bar under it will indicate how much water have you inside.
To use the item simply click the correspondent hotkey from the action bar, or click use in the inventory tab.
Structures that allows you to refill
|Large Water Well|