Genjianswered grow question 2y ago Effects on the plant should be minimal to unnoticeable. I've had an aeroponic system running myself, and the roots grew through the drains into the nutrient tank. The only problem that can arise is that the roots can clog the drain, and you could end up flooding your system. My solution was to simply pull the roots out of the tank and into the root area. This way, the drains are clear again, and everything is good.