I suppose it would depend on what type of plants you have but I keep my water at the level of the clay balls. Im guessing roots get to the water at some point because I rarely water. Occasionally if a plant looks a little dry ill pour some water on it but not very often. Roots of my pothos go into the pond. I think the problem with most people keeping plants is over watering. The drainage layer is there for the health of the plant roots so they don't rot. Sometimes you'll see some potted plants with a layer of gravel at the bottom. Same purpose.