Chemistry in Aquaponics

Take from

One of the most important yet least understood aspects of Aquaponics is the bacteria that we rely on and its function in the nitrogen cycle. I know what you’re thinking, bacteria (or “GERMS” if you watch a lot of disinfectant commercials) are meant to be bad, aren’t they? The fact is that there is good and bad in everything, even down to bacteria. Life wouldn’t be possible without them. Fish excrete ammonia. In a lake or ocean it’s all good because the vast volume of water dilutes this ammonia. When you’re keeping fish at home it needs to be managed as it is very toxic to the fish. Decomposing food also creates ammonia. Some of the effects of excessive ammonia include:

  • Extensive damage to tissues, especially the gills and kidney
  • Impaired growth
  • Decreased resistance to disease
  • Death

Luckily natures got it all sorted! Enter Nitrosomonas sp. This good little bacterium eats ammonia and converts it to nitrite. Now, nitrite is much less poisonous to the fish than ammonia, but it’s by no means a good thing. It stops the fish from taking up oxygen. Natures got it under control again, with Nitrobacter sp. This good bacterium eats nitrite and converts it to nitrate. Luckily nitrate happens to be the favourite food of plants. Also the fish will tolerate a much higher level of nitrate than they will ammonia or nitrite. What you’ve just read is pretty much the nitrogen cycle. When an aquaponics system has sufficient numbers of these bacteria to completely process the ammonia and nitrites it is said to have “cycled”. Your goal should be to establish the nitrogen cycle quickly and with minimal stress on any aquatic life you may already have. Without their respective “foods” these bacteria will not exist in useful numbers.

This is why you will see an ammonia “spike” when setting up a new tank. The bacteria will increase their numbers (reproduce) in response to an increasing ammonia load, so it makes sense that we would see a “spike” before they respond. Shortly after you have ammonia the bacteria will start reproducing and working away for you. The same goes for Nitrobacter sp., they’ll only want to start reproducing and working once Nitrosomonas sp. is comfortable and producing lots of nitrite. Now, while one point you’ve just read indicates that Nitrosomonas sp. won’t process ammonia at pH 6.0 or below, this was determined in a sterile lab culture. Similar research has shown that species of Nitrosomonas sp. in a natural environment such as soil will still process ammonia even at pH 4.0!


This goes some way to explain why some of us have systems that are YEARS old with a pH of 6.0, no ammonia and happy fish. Once a system has a compliment  of micro flora and fauna at work there seems to be an inherent synergy that allows wider environmental ranges to be accommodated. I would definitely recommend that people strive for the above environmental tolerance ranges on initial system set up and the early life of their systems.

Many people with aquaponics systems try to maintain their pH at around 7.0 to 7.2 because this range satisfies the plants, fish and bacteria. The nitrogen cycle itself has a tendency to reduce pH, however it is pretty easy to keep pH at around 7 through the addition of calcium carbonate. Calcium carbonate increases pH, but will stop dissolving at pH around 7.4, meaning pH will stay pretty stable until all of the available calcium carbonate is depleted.


They must colonize a surface (gravel, sand, synthetic biomedia, etc.) for optimum growth.


Ph Vs Nutrient

In both your aquaponic system and in soils, pH effects the availability of nutrients to your plants. As you can see detailed in the chart below, a pH of between 6 and 7 is ideal for availability of most nutrients and minerals. The width of the coloured bars show availability of the nutrient or mineral.


Ammonia Toxicity

Ammonia is toxic to fish at certain levels and with an aquaponic system you must be careful that your fish are not adversely affected by high ammonia levels. The toxicity level depends on a couple of different factors, pH and temperature, as well as the particular fish species your growing. As temperature and pH increases ammonia becomes much more toxic to fish.


Nitrogen Cycle

Our most pirated graphic on the internet, stolen by hundreds of people and palmed off as their own. The original diagram was thanks to Dave in South Africa, Dave designs our magazines and has a great interest in aquaponics and infographics to help get an idea or concept across to people simply. I guess this one does it very well as it’s so popular.