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)

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/

Don't forget the optional voxel models! They did some really cool stuff with Build. I loved some of the creative uses of things like controllable vehicles (sometimes with guns!).

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

No man is island, except Lo Wang.