Maiden: About Wateralpha And Novis
"r_novis" should pretty much always be "0" (i.e. off) -- which is the default anyway, so basically, don't tinker with it. This is why:
What r_novis does, is to tell the engine to ignore
vis data, which specify which parts of the map are visible to the player at any given time.
Vis (short for visibility) saves the engine from having to draw the entire map at all times (which is a waste of resources and, especially on large maps and slower computers, can slow the game down). If a map has
not been designed and compiled with transparent water in mind, then the water blocks visibility, and whatever is below or above the water (from the player's perspective) is not drawn. Simply setting r_wateralpha to a value lower than 1 will not magically make the water transparent -- in Quakespasm you'll get some ugly visual artifacts.
By switching r_novis to "1" and then lowering the wateralpha, you can force the engine to display the water as transparent -- but at the cost of having the engine ignore vis data and drawing the entire map at all times.
Perhaps more importantly, maps that do not support transparent water have often been deliberately designed as such, so if you "trick" the engine into displaying transparent water, you might also end up breaking the gameplay and/or aesthetics of the map you're playing.
So in summary: only ever adjust wateralpha and leave novis alone. If the map has been designed for transparent water, it will work; otherwise stick with opaque water (i.e. wateralpha 1).