The Nitrogen Cycle

A good understanding of the nitrogen cycle is essential in order to construct a successful aquaponic system.  It is basically the process by which fish excrete toxic nitrogen into the water and plants take it out, but let me go into some greater detail about the intermediate steps.

Let’s start with fish.

Fish excrete, just as all organisms do.  However, unlike most other organisms, fish constantly and continually excrete highly-toxic nitrogenous liquid waste from their bodies in the form of ammonia.  If ammonia becomes too prevalent in the water, your fish will die.

Fortunately, however, bacteria in your growbeds collectively called nitrosomonas are constantly gobbling up ammonia and converting it into a difficult compound called nitrite.  Nitrite is much less toxic for fish, and they can therefore endure it in much higher concentrations.  It does, however, inhibit the ability of fish to utilize oxygen.  In high doses, therefore, it can be fatal.

Again fortunately, however, different bacteria collectively known as nitrobacter are also present in your growbeds.  These bacteria aren’t particularly fond of ammonia, but they do love nitrite.  In the process of gobbling up nitrite, these bacteria convert it into nitrate.  Nitrate is not harmful to fish unless it builds up in truly enormous quantities.

And the buildup of such a large quantity of nitrate is extremely unlikely.  Why?  Because nitrate is the compound which plants are able to absorb and thrive upon.


So let me summarize.

  • Your fish eat nitrogen-rich food and excrete that nitrogen in the form of highly-toxic ammonia.
  • You pump this ammonia-rich water through your growbeds, and bacteria convert this ammonia into a less-toxic compound called nitrite.
  • You then pump this nitrite-rich water through your growbeds again, and different bacterial colonies convert this nitrite into essentially nontoxic ammonia.
  • And then plants soak this ammonia up and convert it into amino acids, nucleic acids, and other compounds essential for life.
  • Eventually, you will feed certain organic plant material to your fish, and this cycle will start all over again.

The utilization of this nitrogen cycle is precisely what makes aquaponics so appealing.  It makes produce from waste.


But let me leave you with a few words of caution.

This process is, as it suggests, highly cyclic.  Therefore, you will not see equal and constant amounts of ammonia, nitrite, and nitrate in your system at any given time.  Rather, you will see high quantities of ammonia and a complete lack of nitrites and nitrates.  Don’t’ worry.  As long as this ammonia doesn’t get TOO high (about 0.2-0.4 mg/L), your fish won’t die.  And it won’t be long before this ammonia is converted into nitrite and ammonia levels drop sharply to zero.  Finally, this nitrite will converted into nitrate, as nitrite levels fall in sequence.  In fact, high levels of nitrate should trigger more of a concern than high levels of ammonia, as in a healthy system nitrate should be readily absorbed by plants before it is able to build up in measurable quantities.  This whole cycle takes about four weeks.  You should see regular rising and falling of the concentrations of each of these compounds in your system, and so long as they don’t get too high and drop to zero at some point, your cycle is working fine.  So don’t worry too much.

However, certain signs may indicate that you should worry some.

If the presence of any of these compounds is off the charts (for information on monitoring your system, seem my post), something is wrong.  Either you’re overfeeding your fish, you don’t have enough growspace for sufficient bacterial populations, your fish are overstocked.  Once you identify the problem, you can fix it by cutting down on feeding, adding growspace, or transferring your fish to different tanks, respectively.  Letting nitrogen levels get out of control is especially common when raising fry, fingerlings, or young fish in a small, enclosed tank.  For more information about keeping your young fish well, see my posts under the category keeping your fish happy.


Here is a brief diagram that summarizes what you just learned:

This is a simple diagram of the nitrogen cycle.

This is a simple diagram of the nitrogen cycle.

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