textures/saberpeak_terrain/sp_mediumwater_shader
{
qer_editorimage textures/saberpeak/saberpeak_terrain/sp_mediumwater.tga
qer_trans 0.35
cull disable
surfaceparm nonsolid
surfaceparm water
surfaceparm trans
{
textures/saberpeak/saberpeak_terrain/sp_mediumwater.tga
}
}
Try that. then add the name to the shaderlist.txt open GTK radiant press T go to option Flush & reload shaders.
Go to the map Saberpeak_terrain and look for a texture called sp_mediumwater_shader
I couldn’t get shaders to work either because i selected the texture instead of the shader. so this has to work 
good luck and enjoy 

For further questions you can allways PM me 
Well i’ll explain you a little bit about your shader.
textures/saberpeak_terrain/sp_mediumwater_shader <-- this here is the name of the shader you use in gtk radiant
{
qer_editorimage textures/saberpeak/saberpeak_terrain/sp_mediumwater.tga <-- this here is the image it uses in radiant so you can click on it. most of the time it’s the texture you want to use.
qer_trans 0.35 <-- this makes your shader transparent in radiant
cull disable <-- cull disabled
surfaceparm nonsolid <-- this makes it nonsolid
surfaceparm water <-- this makes it water
surfaceparm trans <-- and this transparent
{
textures/saberpeak/saberpeak_terrain/sp_mediumwater.tga <-- the texture it has to use
}
}