8 days ago - Shurenai - Direct link
Dirty water is a resource that you're unlikely to drink in it's current state; It's primary use is to be crafted into other things. When you're out looting, you'll find a good amount of it, so it stacks higher so it's less of an inventory hog.

Clean water is a Drink item that, like other drinks, is likely to be drunk in it's current state. It's primary use is to be drunk and it isn't found when looting much/at all, and so it stacks smaller to restrict the player's ability to have water on them; If you want more, you commit more inventory slots to it.

It's... kindof like how backpackers and hikers decide what goes in their pack, The restricted stack sizes of items you Want to have in your backpack makes you think about how many and how much of each you want to keep on hand vs open space you want to keep to acquire new items when looting.

Put more simply, It's game balance.