Rain should fill in the holes after a while but you should be able to sleep while it's raining to avoid .. e.g if you wanna fill in a large area with water sources and you don't have a lot of buckets especially early game you could just wait for the Rain but it will only fill in a certain chunk area that will bebe acti where the player is and not really the chunks that are not loaded. It just makes sense and makes the game a bit more realistic.
Maybe if you could let us place buckets on the ground it'll also fill those.
Anyway it's just an idea. I hope it makes it into the game and of course you could test it before see if it's possible.
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