The undergravel filtering systems used in my tanks is primarily for bio-filtration, water movement, and aeration. They have kept my water clear, now along with the HOB filter, for 40 years. Yeah...old school...can't help it. I've never had the "waste" under the filter give me any grief. Clean it out every third gravel vacuuming and I've been ok. Have heard that when the gravel is over a couple inches deep it's easier for the harmful bacteria to "hide" and create trouble. So in recent years I've "thinned" out the gravel a little, and have cruised without incident. Oh, too, I use powerheads to increase through put.