If a completely natural born member of species can not survive in its specified environment comfortably, the developing civilization will not be of that environment and therefore will not be a civilization of that type. If adding water everywhere in civilian spaces is not a completely logical no brain decision, then it is not an amphibious civ, nor a naturally born underwater civilization, it’s just an above ground/underground civilization that happens to be underwater.
If a species edited their biology to comfortably live in conditions different to their naturally born state, though, I think it would only count as underwater/amphibious/land, etc. if they built their whole culture around it and built it from the ground up with that in mind, or is forced to adapt to those conditions.
If this is about metal working, may I refer you to this thread The Holy Grail:… from what I gather we already figured out how to smelt metal we just need a way to work on it underwater. My idea was to have them work on it in air bubbles but that has its own issues, like breathing, temperature, the type of fish and the level they’re working on it at, to name a few, but I’m making progress.