Tried it out again on 9.0-4 and I still get the black water issue, my deck is on latest stable update and using mesa radv 24.0.99 if it helps clarify. Edit: Just checked the mesa github, turns out this is one of those is...
There might be some regression(?) in Proton Experimental, since using the stable Proton 9 (version 9.0-4 at the time of writing) in my system with AMD Radeon RX 7800 XT has the water rendered fine.