Purified water is added to the workshop inventory when the settlement update timer activates every 24 in-game hours (72 real minutes, if the player doesn't accelerate the passage of in-game time by sleeping). Entering workshop mode at a settlement pauses the update timer for that settlement, while in-game time continues to pass, so the exact time of the update tends to shift at settlements that undergo construction.
The settlement timer also controls when drinkable items are consumed from the workshop at the settlement, at a rate of 1 per human population. This consumption takes place before the purified water is deposited at some settlements, and after deposit at others. Drinkable items stored in containers other than the workshop will not be consumed.
Purified water will not be added to the workshop if more than 5 drinkable items (including dirty water and alcoholic beverages) are present. This cap increases by 1 for every four population. Regular collection of excess purified water is therefore necessary to continue production.
Purified water can be farmed as a greater source of caps, due to its unlimited supply.
Additionally purified water can be generated by using the "Fill Bottle" option when next to a water pump or water fountain if there are empty bottles in inventory. The empty glass containers that can be used are all variants of empty bottles.
Unlike the bottled water featured in Fallout 3 and Fallout: New Vegas, the water in Fallout 4 either comes in cans or cartons. This is most likely intended to reinforce the fact that plastic is an uncommon material, and is used in more specialized roles. This is because plastic is made of oil, which was in very short supply during the mid-21st century and prior to the Great War.
There is a random encounter in which the Sole Survivor will encounter a water beggar and will have the option to give the beggar some purified water to ease their thirst.