Beneficial Bacteria and Worms


bacteriaBacteria are the gears of an aquaponic system. The fish would quickly die from ammonia toxicity and the plants would starve for lack of nutrition, without nitrifying bacteria converting the ammonia to nitrates.  Nitrosomonas bacteria convert the poisonous ammonia into nitrites and then nitrospira bacteria convert the nitrites into nitrates.  It takes about a month for the process where the bacteria are naturally established (called “cycling”). After becoming established, bacteria will form on all surfaces of the system that stay in contact with the fish water.

Chlorinated tap water should NOT be used when filling a tank, as chlorine will kill the nitrifying bacteria in the system, please see our Safety Tips for more information. A dechlorinating filter should be used to remove chlorine from tap water, or top off your tanks on a frequent basis with only a very small amount of water (less than 5% of the water volume), or establish a separate de-gassing tank.  Chlorine will “off-gas” (i.e. the chlorine leaves the water as a gas) on its own within a couple days, and more quickly if you add aeration.  Chloramine is also harmful to nitrifying bacteria and the fish and, if present, must be filtered from the water.  Contact your municipal water supply to find out if there is chloramine in your tap water.

The bacteria in an aquaponics system will get better over time (becoming more stable and effective).  It takes bacteria about a month to become established in your system and after 6 months it will outperform many traditional soil based or hydroponic systems.



  • Never letting your grow bed dry out
  • Never exposing the bacteria to freezing temperatures for an extended period of time
  • Never allow the bacteria to come into contact with chlorine or chloramine


Vermicompost is extremely beneficial for the plants. By adding composting red worms to your media-based aquaponics system after a few months to break down the solid fish waste into vermicompost.