Thanks for the information HeelX. Yes I am clipping the not-affected pixels and yes the shader is slow but I'm pretty sure that this isn't caused by the watershader because it 'just' uses some clever math, but nothing too complex.
I think it's the complex & inefficient objectshader I'm using there and the textures because they don't have mipmaps.
EDIT: I just tested it, in the worst case the textures and the specular lighting reduce the framerate by 50% (~120 fps)