This is how the texture looks, the map contains a 3D floor for swimmable water, which is tinted light blue.

the underwater part, however, it'll look like this

Firing a projectile from that weapon, which has a dynamic light on it, makes the nearby walls render properly. Seems like an issue with color mixing.
I tested a bit and I can remove the glitch by removing the sector setting "Desaturation" on the control sector (UDMF format, editing on SLADE3, not sure if that's the proper setting name to refer to)
Sorry if I am jumping the gun a bit since this is not yet merged with the main branch, but seems it shouldn't be a major issue and is a bit of an unusual case that could be missed easily. Actually I left desaturation on by accident, wasn't even supposed to be there.
In case it's hard to replicate I can send the map or the whole project file, but should be a regular body of water just with colored light and desaturation of 0.1 on the control sector. The texture is a png truecolor file, 256x256 in size, shows normally in the pre-glew merge version and after a dynamic light affects the wall. Happens only in the underwater section, everything else renders normally, and also renders normally without desaturation.
By the way, this is probably not a bug and just a limitation of the 3D sector system, but that water flat has a defined glow, which works properly when used as a normal flat, but it won't glow in that 3D sector. Is this normal, or a mistake on my part? (happens in any version)