Flooding the grow bed delivers nutrients to the plants and the bacteria; beds draining beds oxygenates the water, plan plants roots, and the bacteria. When a planting bed is periodically flooded like this it is called a flood-and-drain or ebb-and-flow system and is what most media based aquaponic systems employ.

There are two ways to drain an aquaponics grow bed – timer-based or siphon-based. Timer Based aquaponic systems work by having a timer control when the pump is powered. Typical timing cycles are 15 minutes on,45 minutes off.This works best for very simple systems, or systems that need to be silenced.Siphons work using physics principles and are nice because the pump runs continuously and there is no extra part(a timer) that can eventually fail.