If I remember correctly to get transparent water the level also had to be re processed through the "vis" program with a transparent water flag set.
vis did a precalculation for where a level segment(the partition in binary space partition) could be seen from any other level segment. the end effect was that while glquake did have a option for transparent water, the geometry would not draw on the far side. making the effect useless without a bit of extra work. But I have to admit I have no idea if entities(other players) would draw or not.
Adding: the server and client had to both be running vis patched maps to be able to see other players in the water due to the way entity visibility was calculated server-side.
The downside to running vis patched maps on a server is it used slightly more CPU than unpatched maps IIRC. Perhaps someone that ran more servers than I did (I ran two nodes on an Intergraph InterServe with dual P6-200s) could weigh in on what the impact was at scale.
vis did a precalculation for where a level segment(the partition in binary space partition) could be seen from any other level segment. the end effect was that while glquake did have a option for transparent water, the geometry would not draw on the far side. making the effect useless without a bit of extra work. But I have to admit I have no idea if entities(other players) would draw or not.
update: found this https://quakeone.com/forum/quake-help/general-help/4754-visp...
Apparently there is a no_vis option to run without the visible set optimizations.