Terrain island help please!

[Steamed]

On the tutorial part of this website someone posted a tutorial on how to make a river look good without using ramps. First you must make your river, then fill it in, then use the "Height: Lower" tool to lower the filled in part so the water comes through. It was working perfectly but I have one problem. When i lower the filled in part it lowers the water too, making it so units cannot walk in it! Please help!