Those spots look like they are there because you cut a hole in the ground plane by grouping the negative terrain with the plane. The black spots are then shadows between the terrain plane and the water plane (as they both have no thickness). You should really try to follow roch222's way of doing this as I don't think you will get a natural looks this way. The ground plane simply looks too flat and even though raising the waterplane might help you to prevent the black spots... It still won't look natural.