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Description of your suggestion.

My suggestion is to change the penalty to something else. I would rather have it damage the player character, or even making the character hungry in the process. If drinking water from environment reduces the water in the body, it would be weird even if it's considerably muddy or polluted. Instead, the thirst penalty should be something to do with the day desert biome, specifically when the character is not under the roofs. And the penalty for drinking the dirty water should be direct infection damages.
Drinking water removing the entire 1x1 water source feels weird, setting up infinite water source is already easy enough, so it would be better to not remove the water source upon drinking from there. Just for the visual representation.
Bamboo pump is a thing in this mod, I think a bamboo bottle would be neat.