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/