How to Cycle Your New Aquaponics System

Last Updated on April 5, 2019

System cycle is a process of establishing beneficial bacteria in your aquaponics system. Cycling starts when your fish (or you) first add ammonia to your system.

Many of you are in the process of building your first home aquaponic system or you at least want to start one someday.

You have researched properly to choose your fish for aquaponics and immediately got the best fish to start the aquaponics system. Then you searched about setting up the system and realized you ignored maintaining your system and your fish! So to get started, you need to know a few important things, especially if you’re cycling your tank with fish!

Cycling starts when you add ammonia to your system.

There are two ways to introduce ammonia into your system: with fish and without (fishless). In this article, we’ll talk about cycling with fish.

Fish can die if cycling isn’t done properly. Read How to cycle Aquaponics System without Fish

Kicking off the Cycle: adding the fish

Cycling aquaponics system using fish is the easier of the two methods because there are no extra inputs. However, it is definitely more stressful because live critters are involved.

Graph of ammonia levels
Graph of ammonia levels.
  1. First of all, Add water to your system and turn on the pump (no fish or plants at this stage). Let it run for 2-3 days. This is particularly important while using tap water. Tap water contains chlorine, which takes at least 24 hours to dissipate.
  2. Add some sacrificial fish (cheap species) after 2-3 days. 10-20 goldfish per 1000 liters is adequate. These fish will generate ammonia, as will uneaten food.
  3. If you wish, you can also add some seedlings to your grow beds at this stage, but best to wait a week or two.
Nitrogen Cycle
Nitrogen Cycle

Over the first 10-15 days, ammonia will gradually increase to a peak. Do not feed the fish during this time; they can go 3 weeks or so without food and feeding will only add to the problems. The ammonia is high because bacteria that turn it into nitrites haven’t established enough to quickly start the nitrogen cycle.

Ammonia attracts Nitrosomonas, the first of the two nitrifying bacteria that will colonize your system.

The Nitrosomonas convert the ammonia into nitrites (NO2). This is a necessary step in the cycling process. 25 days into the cycle, the nitrite level will have peaked. However, nitrites are even more toxic than ammonia!

Read about how to Avoid and Treat Nitrite Poisoning in Your Aquaponics System.

But there is good news because the presence of nitrites attracts the second kind of bacteria we require: nitrospira.

Nitrospira converts the nitrites into nitrates, which are generally harmless to the fish and excellent food for your plants. This is the last step in the nitrogen cycle.

Are We There Yet?

Your system will be fully cycled and aquaponics will officially begin once

  • You detect nitrates in your water.
  • Ammonia and nitrite concentrations have both dropped to 0.5 ppm or lower
  • Water testing shows no ammonia and no nitrite despite regular feeding.

So by days 40 to 50, your system should have zero (or less than 1mg/l) ammonia and nitrite. Your nitrate should be 100 plus.

Now, you can start adding more fish to your aquarium. Add fish a few at a time with at least a couple of days in between; your biofilter is now ready to process fish wastes, but your bacterial populations will need to grow along with your fish stocks, and while it happens much more quickly in a cycled tank, it’s still not instantaneous. Adding too many fish at once can still create dangerous ammonia spikes as your biofilter struggles to catch up.

High Level of Ammonia is dangerous for your Fish. For more information, read our post about role of Ammonia in Aquaponics System

Adding Plants

Add plants to your new aquaponic system as soon as you start cycling. Plants are able to take up nitrogen in all stages of the cycling process to varying degrees, from ammonia, nitrites, and nitrates, but they will be happiest when cycling is complete and the bacteria are fully established because good nutrients become available at this stage.

When plants are first transplanted, they tend to establish their root systems in their new environment.

It is just normal if you notice some signs of yellow or dropped leaves initially. There will not be any new growth for a few weeks.

Adding plants to your system right away lets them go through the rooting process early on and readies them to start removing the nitrogen-based fish waste from your aquaponics system as soon as possible.

Experts recommend adding some Maxicrop to get your plants off to a good start during cycling. Maxicrop is derived from Norwegian seaweed, is organic and is used primarily as a growth stimulant, especially to enhance plant root development.

It is extremely effective at giving plants a leg up after being transplanted into your new aquaponics system, is absolutely harmless to the fish, and probably beneficial for the bacteria.

While there are no hard and fast rules about how much Maxicrop to add during cycling, I recommend a quart of the liquid product for every 250 gals. of water. It will turn your water almost black but don’t worry; this will clear up after a week or so.

Monitoring Cycling Process and Tools

Cycling typically requires four to six weeks to complete. With this in mind, as you proceed you need a way to tell where you are in the cycling process.

Specifically, you must monitor ammonia, nitrite and nitrate levels as well as pH so that you know that all these elements are in range, or if not, that you know that you may need to take corrective action.

This is also the only way that you will know when you are fully cycled and ready to add more fish (or your first fish if you have been cycling with no fish at all).

Plus, watching the daily progress of the cycling process is fascinating and something you can only see through the lens of a test kit.

By the way, once you reach the point that your system is fully cycled, you will need to do much less monitoring than during the cycling process.

So, get through the cycling process and look forward to reaping the fruits (or should we say the fish) of your labor.

To do their testing, most aquaponic gardeners use a product by Aquarium Pharmaceuticals called the API Freshwater Master Test Kit. This kit is easy to use, is inexpensive, and is designed for monitoring the cycling process in fish systems. Must-have for Aquaponics and fish tanks.

You will also need a submersible thermometer to measure your water temperature. Temperature affects both the cycling rate and the health of your fish and plants once you are up and running.

Environmental Conditions to Consider

Nitrites are less responsive to surrounding water conditions. But Nitrifying Bacteria responsible for processing are affected by these conditions.

There are many other factors that affect cycling. Read in detail here What are the Water Parameters that affect Aquaponics Cycle

1. Temperature

The temperature for optimum growth of nitrifying bacteria is between 77-86° F (25-30° C). Read more about optimum temperature range in aquaponics here.

2. pH

The optimum pH range for

  • Nitrosomonas is between 7.0-8.0
  • Nitrobacter is between 7.3-7.5

Make sure pH does not drop below 7.0 since nitrification is completely inhibited at 6.0.

3. Chlorine and Chloramines

Before adding bacteria or fish to any aquarium or system, all chlorine must be completely neutralized. Residual chlorine or chloramines will kill all nitrifying bacteria and fish.

4. Light

Nitrifying bacteria are photosensitive, especially to blue and ultraviolet light. After they have colonized a surface this light poses no problem. The bulb that emits UV or near UV light should remain off during this time. However, there is no appreciable negative effect of Regular aquarium lighting.

5. Dissolved Oxygen

Maximum nitrification rates will exist if dissolved oxygen (DO) levels exceed 80% saturation. Nitrification will not occur if DO concentrations drop to 2.0 mg/l (ppm) or less. Nitrobacter is more strongly affected by low DO than Nitrosomonas.

6. Salinity

Freshwater Nitrifying bacteria will grow in salinities ranging between 0 to 6 ppt (parts per thousand) (specific gravity between 1.0000-1.0038).

Adaptation to different salinities may involve a lag time of 1-3 days before exponential growth begins.

7. Micronutrients

All species of nitrifying bacteria require a number of micronutrients. Most important among these is the need for phosphorus for ATP (Adenosine Tri-Phosphate) production. The conversion of ATP provides energy for cellular functions. Phosphorus is normally available to cells in the form of phosphates (PO4). Nitrobacter, especially, is unable to oxidize nitrite to nitrate in the absence of phosphates.

Things to Avoid

  • Don’t use any aquarium products such as water conditioner, algae preservatives or other products for pet fish. It’s not good for you and not necessary or helpful to the aquaponic mini ecosystem.
  • Do not feed much during this time so that less ammonia enters the system, which slows the production of nitrites.
  • Don’t mess with the ph, it will automatically lower over time and you will eventually have to add things to keep it at 7.

Things to Consider

  • You will need a water test kit and you should familiarize yourself with everything you will test the water for by either researching online, reading books or asking someone knowledgeable. I recommend the API master test kit (not the test strips) as a good place to start. Knowing your water conditions is very important.
  • Add salt (when cycling with fish only.)
  • You might also want to consider these fish as sacrificial and perhaps use inexpensive fish from the pet store.
  • Add a handful of composting red worms to grow bed once your system is fully cycled and fish have been added.


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