The Top 10 Reasons Why Your Aquaponic System Isn’t Cycling

By Sylvia Bernstein
Published: December 3, 2019 | Last updated: April 30, 2021 12:41:45
Key Takeaways

Having trouble getting your aquaponic system to cycle? Consult Sylvia Bernstein's following checklist to help identify the problem and start cycling successfully.

When it comes to starting up -- or cycling-- your aquaponic system, both with and without fish, establishing the nitrogen cycle is the hardest, most frustrating, part of aquaponics. This is in part because the activity is invisible to the naked eye.


We hope the nitrifying bacteria are finding our system and then moving in and reproducing, but the only way we know what is happening is through subtle changes of color in a test kit test tube. And when that test tube stays the same color day after day, sometimes week after week, the process can be frustrating.

Over the past few years of handling customer calls about cycling, I've developed a checklist of what to ask to help people identify the problem and cycle successfully.


1. Cold Temperature

During the colder months of the year, this temperature is the number one issue we see, especially with people who are cycling without fish. The optimal temperature for bacteria reproduction is between 77 to 86°F.

At 64°F their growth rate is decreased by 50%. This means the rate at which you cycle will be twice as long as it would be with warmer temperatures. Even if you plan on growing cold or cooler water fish once you are fully cycled, do yourself and your bacteria a favor and heat the water now.

Read More: Introducing Aquaponics - Grow Your Own Fish Sandwich


2. pH Too Low

We had a call just recently from someone who had spent two months cycling with no trace of nitrites or nitrates. The average temperature of his system was between 65 and 70°F, so that could have had something to do with it.

But when we asked him what his pH was, he said 4.0! That is essentially an acid bath and there is no way that the nitrifying bacteria are going to colonize in that kind of environment.


Bacteria prefer a pH closer to 8.0. While this is too high for your plants to be happy, during cycling, the bacteria are the main focus so targeting a higher pH than you will want during the rest of your system's life makes sense. As an aside, if you are using the API Freshwater Master Test Kit, and you see a reading of 6.0 that means that your water is at 6.0 or below. You might want to find another means to test to an even lower range to see what your actual, true pH reading is.

3. Chlorine in the Water

This chemical is added to municipal water supplies to sterilize it and kill bacteria. It is easy to remove because it dissipates from the water as a gas. If you don't already have a de-chlorinating filter on your incoming water supply, you can get rid of chlorine by simply holding the water in a separate tank for a day or two.

Oxygenating the water using an aerator will speed up the process. Or you can use an additive that will de-chlorinate your water—just be sure that it doesn't have any sodium as most of the de-chlorinating solutions made for aquariums do.

4. And Chloramine

While you can assume your city water supply has chlorine in it, chloramine (a derivative of ammonia by substitution of one, two or three hydrogen atoms with chlorine atoms) is rare and is also much more difficult to get rid of. There are two ways that I know of. The first is a double mechanical filtration method where you send the water through both a charcoal filter and a reverse osmosis filter.

The second is to remove it chemically by adding a product such as ChloramX. If you are using the chemical method, you should do this in a separate holding tank before the water enters your aquaponic system.

Read More: 3 Aquaponic Stress Factors

5. Adding Too Much Ammonia

The next problem we see only occurs during fish-less cycling, and the scenario unfolds as follows: you add enough ammonia to reach 4.0 ppm then you start testing your system every day. After a while, the ammonia disappears and nitrites show up.

Good news! The problem starts, however, when you don't replenish the ammonia. Think of the ammonia as food that you set out to attract the first set of nitrifying bacteria (nitrosomonas), and those bacteria come to the party bringing the food (nitrites) for the second set of bacteria (nitrospira). If the food runs out, the party is over and everyone goes home.

You need to keep up a steady supply of ammonia in the front end of the process to keep everyone happily reproducing and colonizing your system. That steady supply can come either from an ammonia compound or from the addition of fish to your system.

6. Aiming for 6ppm Ammonia

Some aquapons believe that ammonia levels higher than 6 ppm will actually retard the cycling process. Some don't. I have yet to form a strong opinion either way, but I thought I would add it to the list of possibilities.

7. Too Clean of an Environment

Occasionally, we find a system that is being started in an indoor environment so shut off from outside air and a natural supply of nitrifying bacteria that it will never cycle on its own without the addition of purchased bacteria. This is referred to as a sterile environment. I've seen this problem occur both in schools and when people are growing in interior rooms of their house.

8. A Lack of Oxygen

Nitrifying bacteria are aerobic. The more oxygen you have flowing through your system, the faster your system will cycle. Be aware that this is challenged by my first point. Liquids at higher temperatures have a harder time holding gas, so if you are heating your water to encourage bacteria growth, be sure to pump up the oxygen as well.

Read More: Swirling Oxygen - Is Your Aquaponics System Circulating Properly?

9. Rushing for Results

Cycling is a natural process we can certainly encourage by establishing favorable conditions, but after that, Mother Nature is on her own schedule. You might be doing everything right, and the bacteria just need a bit more time.

10. You Really Are Cycled, You Just Don't Know It

This is my favorite, because it is so easy to fix and the customer is usually delighted to discover that their problem was not really a problem at all. The instructions for your test kit need to be followed to the letter.

If you don't follow them, you won't get accurate readings. The nitrate test is by far the most complex in the API Master Aquarium Test Kit, and therefore the most likely to tell you that you don't have any nitrates when, in fact, you actually do.

Read, and carefully follow, instructions! Or get a hold of a digital meter and say goodbye to complex instructions and color chart comparisons.

Cycling an aquaponic system can be a trying time, but the good news is that once you are fully cycled, you can safely add fish and plants and will never need to go through this again! Good luck.

Read More: How to Start an Aquaponics System Part 1


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Written by Sylvia Bernstein

Profile Picture of Sylvia Bernstein
Sylvia Bernstein is the author of Aquaponic Gardening: A Step by Step Guide to Growing Fish and Vegetables Together. She is also the former president of The Aquaponic Source, and the co-founder and past vice chairman of the Aquaponics Association. Before discovering aquaponics, Slyvia was the vice president of marketing and product development for AeroGrow International.

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