There is an optione "enforce water height limits". If you disable it these kind of things can happen, but you have a lot more options to use water.
You could copy and paste the water, so it covers a greater area. After that use the cliff tools to recreate the cliffs you want. The problem here is, that the water is too small, so you need to increase the water area. After that you can add cliffs wihtout actually decreasing the water area. The water will just be below the cliff.