How to Cycle Your Aquaponics System

How to Cycle Your Aquaponics System

If you’re an aquaponics beginner planning to build your own system, one crucial question that comes to mind is how you cycle a newly built aquaponics system. Well, worry no more because this blog will discuss ” system cycling,” the different cycling methods, and how to do it in your new aquaponics system. 

What is System Cycling in Aquaponics?

System cycling is establishing a bacterial colony in new aquaponics systems. This process involves constantly introducing an ammonia source into the system, feeding the new bacterial colony, and creating a biofilter. Ammonia is required for the nitrifying bacteria to begin their work and reproduce. The ammonia can be generated by the fish or added using other methods. 

The nitrogen cycle converts the ammonia from fish waste and decomposes fish food into plant nutrients. However, for this conversion to occur, nitrifying bacteria must be present. The cycling progress is measured by monitoring the nitrogen levels. 

These nitrifying bacteria first convert the ammonia into nitrites and then into nitrates, which become food for the plants. Your new aquaponics system is considered fully cycled when the nitrate levels increase steadily, and the ammonia level is less than one ppm. The nitrite level is zero ppm during testing.

It is important to note that the ammonia and nitrite levels will be high during the cycling process, which could harm the fish. Also, ensure that the system, including the fish tank and biofilter, is protected from direct sunlight before starting the cycling process.

How to Cycle Your Aquaponics System

System Cycling Tools

These tools are essential in the cycling process. During cycling, you must monitor your system’s ammonia, nitrite, nitrates, and pH levels to know if these elements are within their acceptable range. You can take corrective action immediately to avoid more problems if they are not. These cycling tools will also help you know when your aquaponics system is fully cycled and ready for more fish. 

These are the tools you need for cycling your aquaponics system:

  1. Freshwater Master Test kit tests ammonia, nitrites, nitrates, and pH levels.
  2. Submersible thermometer to measure your water temperature.

Things to Consider Before Cycling a New Aquaponics System

  • Knowing your water condition is very important, so use a reliable water test kit. You must also familiarize yourself with the process of performing water tests and reading the results. 
  • If you use the cycling with the fish method, consider using an inexpensive fish as a sacrificial fish. 
  • Once your system is fully cycled, consider adding composting red worms to your grow bed.
  • Avoid using aquarium products such as water conditioners, algae preservatives, and other products for pet fish.
  • Do not feed much during cycling. Don’t worry; fish can survive without food for a few days.
  • Do not mess with pH. 

The Different Methods of Cycling

1. Cycling With Fish

Cycling with fish is the old method of cycling new aquaponics systems and can take 25-40 days. It is because the nitrifying bacteria grow relatively slowly in this method. 

Steps on Cycling with Fish

After adding the water, turn on the pump and let it run for 2-3 days. 

  1. After 2-3 days, start fish cycling by adding a few fish to the fish tank. Add only a few fish because too many will cause the ammonia levels to spike and harm the fish. 
  2. Once your fish are in, feed them lightly to start producing waste and start the cycle.
  3. Monitor the ammonia, nitrite, and nitrate levels daily to ensure they do not get too high. If the ammonia level is more than 3.0 ppm, you must do a partial or complete water change to avoid an ammonia spike. Ammonia should remain below 3.0 ppm, nitrite below 1.0 ppm, and the nitrate level should increase over time.
  4. Continue monitoring ammonia, nitrite, and nitrate levels and replace the water as needed until your fish tank is fully cycled. Your aquaponics system is fully cycled when your ammonia and nitrite levels remain below 0.25 ppm.
Speeding the Cycling with Fish Process

Alternatively, if another aquaponic system is available, it is beneficial to share part of the biofilter as a seed of bacteria for the new system. This greatly decreases the time necessary for cycling the system. It can also be helpful to separately start a biofilter medium by continuously trickling a solution containing 2–3 mg/liter of ammonia a few weeks in advance. 

The media would then function as a primer by simply incorporating it into the new aquaponic biofilter. A simple trickling system can be built by suspending a wide plastic crate of medium above a small tank containing the ammonia solution that is being circulated by a small aquarium pump.

2. Fishless Cycling

Fishless cycling has become the most popular method of cycling, a new aquaponics system today. It takes a few days and offers more advantages over cycling with fish. First, the grower and the fish will endure less stress while cycling. Second, there are no fish involved in the process, so you don’t need to be overly concerned when ammonia, nitrite, and pH levels go up.

Sources of Ammonia for Fishless Cycling
  1. Liquid Ammonia: If you plan to use liquid ammonia, ensure that it is pure ammonia (5 -10%) and water. Don’t use ammonia with perfumes, soaps, colorants, or additives. These additives could be detrimental to the fish and plants.
  2. Ammonium Chloride (Crystallized Ammonia): This is effective as the liquid ammonia. You can purchase this from any aquarium supply store. 
  3. Urine: Human urine or any animal urine is a good source of ammonia. To use urine as your ammonia source, you should put it into a sealed bottle for three weeks to allow the urine to turn into ammonia before adding it to your system. If you add fresh urine into your system, you will not be able to track how much ammonia is going into the system. Your ammonia levels will read very low with fresh urine at first but will suddenly increase or explode after a few weeks, which is not suitable for your system.
  4. Dead Fish: Using a dead fish as an ammonia source is not ideal because of the danger of allowing other bacteria or chemical compounds to enter your system. Dead fish may also attract flies and other insects, which are not good.
Steps of Fishless Cycling
  1. When your aquaponics system is ready, begin by adding an ammonia solution a little at a time to the fish tank until your reading from the ammonia test is -5 ppm.
  2. Record the amount of ammonia it took to reach the -5 ppm and then add that amount daily until the nitrite appears at 0.5 ppm.
  3. Once nitrites appear, cut back the daily dose of ammonia to half of the original volume.
  4. Once nitrates appear at 5 – 10 ppm and nitrites have dropped to zero, your system is fully cycled, and you can start adding your fish.

3. Cycling by Using Bacteria from an Established Aquaponics System

Using sludge from an established aquaponics system’s grow media or filter is a quick and effective way of establishing bacteria in your new system. Just ensure that the bacteria that come from an established system are healthy because diseases can easily be transferred from one system to another.


Adding Plants and Fish


You can add plants to your new aquaponics system as soon as you start cycling. Adding plants right away will let them go through the rooting process early on. Initially, you may notice some signs of nutrient deficiency, but this is normal. But once your system is established and starts producing the nutrients, they will become healthy and bear good fruits or harvest. 


Although cycling with fish can take longer than other cycling methods, this option is the easier and safest method because there is no extra input involved. Start by slowly adding a few fish to your system. You can start adding the fish once your new system’s ammonia and nitrite levels are below one ppm.

Conclusion: Which Cycling Method to Choose?

In choosing what cycling method to use for your new aquaponics system, you need to consider the availability of pure ammonia in your location. Fishless cycling might be the less complicated method, but the cycling method with fish will be your best alternative if you can’t get pure ammonia. However, if pure ammonia is readily available in your location, the fishless cycling method is an excellent choice because it is less stressful for you and your fish.

System cycling only needs to be done once, so you will not have to deal with it again once you’re done. But once you’ve successfully cycled your new system, all you need to do is regular maintenance, plant your favorite vegetables, harvest, and enjoy the fruits of your labor.