I am not sure it's suppost do to, but when i have potion called something protection lava, i'm still taking damage by drowning. It's suppost do to or not, because previously version of Minecraft it's not should do
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It was the same in earlier versions, it just didn't show the bubbles, but you started taking damage after a while. Tested in 1.2.10.
Use a potion of water breathing if you don't want to drown.
Moved to the correct project.