Later on, in Shadow Warrior, you could even do that, i think they used portals to implement it and i remeber it was a pain to set up in the editor.

That did give us our first software rendered transparent water rooms though (Quake had the water opaque unless you had 3DFX card IIRC)

	▲	mrob an hour ago \| parent [-]
		GLQuake introduced the r_wateralpha setting, which allowed transparent water, but the maps were still compiled with visibility calculations that assumed the water surfaces were opaque. You got visual artifacts unless you enabled r_novis to ignore the pre-calculated visibility calculations. Modern computers can handle it, but this was a heavy performance cost at the time. To work around this, people used an unofficial tool to patch the maps to support transparent water: https://vispatch.sourceforge.net/

Yes, essentially with a second rendering pass. Not cheap to implement which is why the game used it relatively sparingly.