Simply stated, I don't. The tank uses the waste from my fish and my fish food as fertilizer for the plants. I use a gravel vac for water changes once in a while since it is what I have for a siphon. I simply vacuum above the substrate's surface and do not remove anything below the surface. That tank is set up with both potting soil and a cover of gravel in layers using the Walstad approach so if I did a deep gravel vac I would be tearing up my substrate that I so carefully built. The tank stays fairly neat and clean by me allowing the excess food to decay to provide plant nutrients. If things start to build up a bit, I back down on the feedings to let the bacterial breakdown of the food catch up. This tank is not run on standard un-planted principles and is not run in a manner that a typical high tech plant person would appreciate either. It is run using a third method, advocated by people like Diana Walstad, that results in great health of both the fish and the plants without other significant chemical inputs outside of the fish food I use. It is not something that I would want to try to describe without referring you to her book. She takes the time to walk you through a few dozen pages before advising a particular item for consideration. Trying to blindly follow her approach, without understanding the science behind it, would probably result in failure.