Understanding Ammonia in Aquaponics

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Ammonia in Aquaponics

Ammonia, along with iron, is an important player in an aquaponics system. Being one of the primary fish products, Ammonia is important to understand.  Hopefully this post will help you understand Ammonia and ammonium. We also want to rid some of the common misconceptions regarding it.



What is Ammonia?

Bright's fish house!

Bright Agrotech’s fish tanks. In these tanks, Ammonia is created as a result of the breaking down of proteins.

Ammonia is a colorless gas. This nitrogen and hydrogen compound is produced by fish in an aquaponics system. An indicator of ammonia is its distinct, pungent smell. The gas is toxic but necessary to give plants in a system the proper nutrients they deserve.

Ammonia is unavoidable in aquaponics systems.

In aquaponics, ammonia and ammonium result from the breaking down of proteins in fish tanks. Fish can eat and digest protein turning it into simpler nitrogen compounds. Once the protein is in the fish, bacteria begin to break down the protein. The end product: Ammonium, NH4+.

Difference between Ammonia and Ammonium


Ammonia contains 1 nitrogen atom and 3 hydrogen atoms and has no charge

Ammonia: NH3

  • Ammonia is more toxic than ammonium.
  • Ammonia is a soluble gas. It has no charge.

Without a charge, cells within the fish cannot regulate ammonia.



Ammonium: NH4+

  • Scientifically, ammonium is the product of ammonia interacting with a proton, positively charging the ion.

    Ammonium contains a positive charge, 1 nitrogen atom and 4 hydrogen atoms.

    Ammonium contains a positive charge, 1 nitrogen atom and 4 hydrogen atoms.

  • Ammonium is a byproduct of the metabolism of animals. Fish excrete it directly into the water.
  • Due to the positive charge, fish are able to regulate the substance in and out of their cell membranes.

Ways Ammonium Enters the System

This gas, although toxic, is inherently part of the aquaponics system. There are several ways ammonium enters a system:

  1. Through the gills of a fish
  2. Excreation from the fish

Both these ways bring this necessary “nutrient” into play.

Aquaponic systems require nutrients to help the plants grow. Ammonium provides adequate nitrogen to plants.


A pH scale

This scale shows the different ranges of pH in streams and precipitation. We recommend shooting for a 6-6.4 level of pH in your system.

pH and Ammonia/Ammonium Levels

To understand ammonia levels you must first understand pH.

  • The higher pH in a system, the higher level of ammonia and subsequently lower level of ammonium.
  • The lower pH in a system, the lower level of ammonia and subsequently higher level of ammonium.

In your system you want to aim for a relatively low level of pH, making ammonium the dominant substance in the system.

Nitrification efficiency is a problem many people run into. A higher level of pH increases the oxidation efficiency in a new system. Generally folks will gravitate toward having higher pH in their system. However, as the system gets older it adapts and efficiency can be reached at lower pH values.

We suggest a good pH level to shoot for is 6-6.4

Once you begin your system it would be intriguing to run at a high pH to increase efficiency. Disregard this urge and stick with a lower level to keep a good balance between ammonia and ammonium.

How to Reduce Ammonia Levels

Ways to bring down ammonia in aquaponics:

1. Reduce the amount of nitrogen going into your system *

  • If you over feed, ammonia levels will jump up. To avoid this, cut back on feeding that tank.
  • A dead fish at the bottom of a tank will secrete ammonia, do not feed this tank for a day.
  • Dead fish or rotting feed are red flags for increased levels of ammonia. Check your system if you’re undergoing an ammonia spike.

2. Increase nitrification efficiency *

This method increases the rate at which your ammonia or ammonium is being oxidized, speeding up the conversion of them into nitrates  which plants can pick up. Try to have nitrates in your system. They are non toxic to fish.

Hopefully this blog helps you further understand the complexity of ammonia and ammonium in aquaponic systems.

Learn More:





  1. What is bad about carbonates in an aquaponics system

    • The videos and discussion is very interesting. Going back to the ammonia topic, one month ago, my aquaponic system had 0 levels of ammonia and nitrite and 80 ppm for nitrate. I measured these levels again this morning and found out that Ammonia and Nitrites are still in 0 but Nitrate is also at 0 PPM. Does it make sense?

      • That makes sense if you’re not feeding aggressively and your plants are nitrate hogs. Oftentimes, however, when nitrates come back as 0, there is usually a testing error.

        • Thanks Chris. Indeed, it was a testing error. Nitrate level is over 40 ppm. Thanks

  2. Why are carbonates bad?

    • PH is at 7.4

    • Carbonates build up in your system and do weird things over time. However the worst thing they do is buffer your pH at a relatively high value, so it makes it tough to bring pH down, and when those carbonates are fully consumed, it can cause your pH to crash.

  3. I read a paper by Dr. Wilson Lennard in Australia who said you should have your system at this lower pH. I thought his argument made a lot of sense and he is also a PhD, but everyone else seemed to suggest neutral is where you have to shoot for. So thank you nick for being my second opinion on that even if you aren’t a PhD I am sure that Dr. Storey approved this which makes it my second PhD.

  4. I loved this video. I got a crash course on aquaponics. Thanks..all of it was spot on regards to the pH and Ammonia and Ammonium.

    • Glad to hear it, Urbancampers! Please let us know if you have questions on topics which we haven’t discussed yet. We’ll do our best to create an article or video!



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