blendFunc GL_dst_color GL_one
those lines make the texture in the stage be transparent, it makes all white colors be transparent.
You need to make a new image or darken your current one so that it has less white to remove. You dont have a specific way to control transparency from the shader itself afaik.
You can also make a new image with an alpha channel(.tga), then the part of the shader that makes use of the image would be something like this:
...
{
map textures/YOURMAP/water.tga
blendFunc GL_SRC_ALPHA GL_ONE_MINUS_SRC_ALPH
...
}
...