Fish in a tank produce waste, which is high in ammonia, a chemical compound toxic to the fish in high quantities. However, the waste water is pumped from the fish tanks, through a small filter, and into the grow bed. In the grow bed, bacteria convert the ammonia into nitrite, followed by another strain of bacteria which converts the nitrites into nitrates. The nitrates are taken up by the plants as fertilizer. This process cleans the water of the harmful ammonia compounds for the fish, and the clean water is returned to the fish tanks. This completes a full cycle of water through the system.
The chemical balance of the system is a little tricky to get started; getting the pH levels balanced, the bacteria colonies established, and the dissolved oxygen levels high enough for the fish to survive are probably the most challenging aspects of aquaponics. Several other problems can also occur such as algae growth, lack of essential bacteria, and swings in temperature or sunlight. However, once stabilized, the system can theoretically run for an indefinite amount of time with the necessary inputs.
The media bed system generally contains a gravel-sized variety of expanded clay or shale. This gives the plants a stable material to allow their roots to grow and also provides a place for the nitrifying bacteria to live. Worms can be added in the layers of media for increased nutrient production. The media bed also uses a bell siphon to create a flood-and-drain effect. In other words, the grow bed is flooded with water to the height of the standpipe within the bell siphon. Next, the siphon starts, and the bed is drained until air breaks the siphon. The cycle then repeats itself. The alternating wet and dry periods allow the plant roots to get substantial amounts of nutrient-rich water and oxygen.
The floating raft system is a Deep Water Culture system in which a buoyant raft floats in a constantly flooded grow bed. These rafts support plants in net pots a couple inches above the water and can be made of corrugated plastic board, XPS foam, EPS foam, or any other sturdy nontoxic material that can float on water. Having the lower part of the roots constantly submerged in the grow bed water allows for a steady supply of nutrients to the plants.