How To Cycle an Aquaponic System: Beginner’s Guide

Aquaponics is the system of choice for farmers or hobbyists who want an efficient, sustainable, and profitable form of agricultucyre. In this food production method, you’ll integrate aquaculture (fish farming) and hydroponics (soil-less farming) for nutrient recycling and waste management. If you’re a beginner, you might now be wondering how to cycle your Aquaponic system.

Here’s an effective way of cycling your Aquaponic system:

  1. Set up and run your Aquaponic unit.
  2. Introduce ammonia to the system.
  3. Add plants and fish to the system.
  4. Speed up the cycling process.

Proper system cycling contributes to a successful Aquaponic unit. The rest of the article will discuss an ideal way of cycling an Aquaponic system for the best results. But, before we get to the nitty-gritty of cycling an Aquaponic system, let’s first understand what this process entails.

What Does Cycling an Aquaponic System Mean?

Cycling an Aquaponic system means introducing and growing a bacterial colony when setting up a unit. Aquaponics is an integrated form of agriculture involving plants and fish. Hence, the bacteria bridge the gap between the macro-organisms by converting fish waste into beneficial forms for plants.   

The bacterial colony acts as a biofilter in any Aquaponic unit. So, they carry out biological filtration of the ammonia present in the fish waste since its accumulation is toxic to the fish. Then, the bacteria convert this waste into less harmful nitrates and a good source of nutrients for the plants in the system.

The process involves the conversion of nitrogen into different forms. Therefore, we can also refer to system cycling to maintain the nitrogen cycle. And, it’s crucial to monitor the levels of these nitrogenous compounds to ensure that they’re within the recommended range.

System cycling can be a slow process, as building the bacterial colony takes up to six weeks. Moreover, the process involves continuously adding an ammonia source to nourish the nitrifying bacteria. Hence, patience is paramount, especially for newbies who’d be anxious to get instant results from their Aquaponic units.

That said, let’s have a detailed look at the system cycling process in an Aquaponic unit.

1. Set Up and Run Your Aquaponic Unit

Before you cycle your Aquaponic system, you must ensure that it’s well set up and running. Hence, if it’s your first time, establishing your unit is the first and most crucial step in this process. Moreover, your unit’s layout will depend on what type of system you’d prefer.

Regardless of what type of Aquaponic system you’ll choose to establish, your unit must have these essential components:

  • A fish tank – houses your fish stock
  • A grow bed – where you grow the plants
  • A water pump – aids in circulating water throughout the system

But you’ll need additional components in your layout, including mechanical filters, air pumps, canals, substrate, or aeration devices, depending on the specific requirement of your system. Hence, assemble them to set up your unit after ensuring that you have all the materials.

Once the set-up process is complete, fill the system with water and leave it overnight to check for leaks. If so, identify the source of the leakage and fix it accordingly. After determining that the water flow is okay, turn on the water pump and let it run the system for about two to three days.

If using tap water, allowing your pump to run the system for this period will dissipate any chlorine in the water. Also, test the water parameters, including pH and temperature, to ensure that they correspond to the environmental requirements of the organisms (fish, plants, and bacteria) that you intend to introduce into your system. But it’s not advisable to introduce your fish or plant crops in your unit at this stage.

To test your unit’s parameters, I’d recommend purchasing a freshwater testing kit by Aquarium Pharmaceuticals Inc. (API) like the API Freshwater Master Test Kit (available on It’s an all-inclusive kit with specific test solutions for measuring pH levels and the amount of different nitrogenous compounds in a system, including ammonia, nitrite, and nitrate. It’s also cost-effective, easy to use, and ideal for Aquaponics.

So, when you’re satisfied that your system is up and running, it’s time to start cycling it!

2. Introduce Ammonia to the System

As I mentioned earlier, system cycling entails introducing and building a bacterial colony in your Aquaponic unit. Now, since the bacteria feed on ammonia, you need to first introduce this nitrogenous compound into your system to attract nitrifying bacteria to facilitate the nitrification process. But this process involves two steps and two types of bacteria for the full conversion of fish waste (ammonia) into nitrates (plant fertilizer).

Nitrification requires a high oxygen concentration since the nitrifying bacteria break down ammonia to release nitrogen. Then, the nitrogen has to combine with oxygen to form nitrite (first step). Hence, your system requires a sufficient source of oxygen, either from an air pump or aeration devices (air stones).

The first type of bacteria that ammonia attracts is the Nitrosomonas, which convert ammonia to nitrites. Nitrosomonas are ammonia-oxidizing bacteria (AOB) that you can find naturally in the atmosphere, land, or water. So, once you add an ammonia source into your unit, the AOB will inhabit the system and start forming a colony in 5-7 days.

Now, you need to continuously add ammonia to your system to keep the AOB well-nourished and grow the colony. However, you should do this cautiously not to exceed the recommended levels, as this will harm the colony. As the bacteria feed on the ammonia, they’ll break it down to nitrite within the next 5-7 days.

As the nitrite levels increase in your system, this will attract the second type of nitrifying bacteria, the nitrospira. These are nitrite-oxidizing bacteria (NOB) that convert nitrites to nitrates. So, once they inhabit your system and start forming a colony, the nitrite levels will eventually decline.

In the next 25 to 40 days, the NOB will fully convert the nitrites to nitrates, marking the end of the nitrogen cycle. So, when you test your unit’s parameters and notice high nitrate levels, this will mean that your system comprises a viable colony (biofilter). However, this duration may vary, depending on some factors, including environmental conditions, the type of ammonia source, and water quality.

Water temperature, for instance, is a significant determinant of how long a bacterial colony takes to multiply. The ideal temperature range for bacterial growth is 24°C to 26°C (75.2°F to 78.8°F). Therefore, water temperatures beyond this limit will slow down the feeding and multiplication of bacteria. Also, ensure that the temperature is between 21°C to 24°C (69.8°F to 75.2°F) once the cycling process is complete, as this is the best range for both plants and fish to thrive.

Now, have you been wondering where to source the ammonia to attract nitrifying bacteria to your system?

Well, you can either introduce fish into your system or use a fish-less ammonia source. However, some Aquaponics farmers opt for a quicker alternative, where they obtain a bacterial ‘seed’ from another unit to build their biofilter. Therefore, this reduces the time to grow a bacterial colony or cycle the system.

Now, let’s have a brief look at the two major sources of ammonia:

Fish Cycling

Most commercial and experienced Aquaponic farmers prefer this method, as they’re acquainted with the recommended parameters. So, fish cycling involves introducing sacrificial fish (they might die in the process) to your system to produce wastes that contain ammonia. Goldfish is the preferable fish breed to initiate in cycling as it’s cheap and tolerant to high ammonia concentrations.

Before adding fish to the fish tank, ensure that the conditions are ideal for their growth. Therefore, the pH should be less than 7.5, while the ammonia, nitrite, and nitrate levels are zero. Moreover, you’ll have to acclimate the fish to their new environment a few days before introducing them into the system.

To acclimatize the fish, follow the steps below:

  1. Transport the fish in containers containing the original water to minimize stress.
  2. Place the sealed transport bags (containing the fish) in the culture water for about 15 minutes to introduce your fish to the new environment’s temperature.
  3. Add some culture water into the transport water slowly for another 15 minutes.
  4. Let the fish stay in a small aerated tank containing the original water for a day. Then, add the new water slowly to the original water, ensuring that the pH level difference between the two isn’t more than 0.5.
  5. Add the fish to the Aquaponic unit’s fish tank.

As you add fish to the system, the air pump or aeration devices should already be in place to provide enough oxygen. Then, you don’t have to feed the fish in the first few days to prevent a sudden upsurge of ammonia into the system. So, you can feed them lightly after 2-3 days after ensuring that they’re now well acclimatized to the new environment.

Fish feed and the water contained in the fish tank will be the main source of nitrogenous wastes in the system. Hence, the type of diet that you’ll choose for your fish will determine the type of wastes they produce. Additionally, since some food will remain uneaten, it decomposes in the water, adding to the fish feces waste.

Now, the ammonia levels in the water will start rising when the fish start feeding and producing wastes. Therefore, using your test kit, measure the ammonia level in your system after 10 to 15 days. If using the API Freshwater Master Kit, the ammonia strip will turn dark green, indicating a high ammonia concentration in the system.

The presence of ammonia in your Aquaponic unit indicates the beginning of the cycling process. However, the ammonia level should not be more than 3.0 ppm, which is toxic to the fish. Therefore, you can now wait for the nitrifying bacteria to inhabit your system or introduce a bacterial ‘seed’ to initiate the growth of a bacterial colony.

After that, you should have daily parameter checks on your system to determine whether nitrification occurs. Hence, be well-informed on the optimum levels to expect for ammonia, nitrite, and nitrate at each stage. Also, monitor your fish and change the water frequently.

If a bacteria colony has started forming, the AOB bacteria will begin converting ammonia to nitrite. Therefore, the nitrite strip will appear dark purple while the ammonia strip will be light green. Hence, this will indicate that the ammonia concentration is decreasing as the nitrite increases.

After a few weeks, the nitrite levels will start reducing as the nitrate concentration increases. So, the nitrite strip will be pale purple, while the nitrate strip will change from yellow to orange and later light red. This indicates that the cycling process (and nitrification) is complete.

Fishless Cycling

If you don’t want to go through the stress and hustle of acclimating fish to the new environment (and losing some), go for the fishless alternative. Fishless cycling is currently a sought-after method for introducing ammonia to a system, as it takes a shorter time. Moreover, you don’t have to worry about spiking ammonia, nitrite, or nitrate levels.

Fishless cycling involves obtaining ammonia from other sources (apart from fish). The ammonia then attracts nitrifying bacteria to the system to initiate the nitrification process. Fishless cycling takes about three to six weeks when the temperature is between 24°C and 30°C (75.2°F and 86°F).

Ammonia sources include the following:

  • Pure liquid ammonia – it contains about 5-10% ammonia in water. Ensure that the ammonia you purchase doesn’t contain any perfume, detergents, or surfactants. These additives could be toxic to the organisms in your Aquaponic unit.
  • Ammonium chloride – it’s a form of crystallized ammonia that you’ll find in most aquarium shops. It’s an effective ammonia source but best suited for aquariums.
  • Organic fish fertilizers – contain both nitrogen and ammonia. For instance, fish and seaweed Neptune’s Harvest Fish and Seaweed (available on is an ideal organic fertilizer. It’s easy to mix (dilute) and apply. The fertilizer is also a good source of nutrients for numerous types of plants.
  • Urine – human or animal urine is a good source of ammonia. However, you need to keep it in a sealed bottle for a couple of weeks (around 3) to convert urine to ammonia.
  • Dead fish – contain ammonia. But this isn’t the best source of ammonia as dead fish may also attract other types of bacteria, apart from the nitrifying species. Moreover, they’ll also appeal to flies and other insects that’ll inhabit the system and disrupt the cycling process.

After identifying the ammonia source that works best for you, you need to introduce it to the system to initiate the cycle. So, here’s the procedure of how to undertake fishless cycling:

  1. Measure about a cupful of your ammonia, approximately 20 ml (0.68 oz) and add it to your system. Note down the amount of ammonia that you’ve introduced. However, this will depend on the ammonia source and the size of your Aquaponic unit.
  2. Wait for around 60 to 90 minutes before you test the ammonia levels in your unit. The recommended ammonia concentration at this stage should not be more than 4.0ppm. This is because a higher concentration will be toxic to the nitrifying bacteria, destroying the colony.
  3. If the ammonia concentration is less than 2.0ppm, you need to add more ammonia to nourish the bacteria. So, go back to the amount you’d recorded, and using the concentration you’ve obtained after the initial test, calculate how much ammonia you need to add to get around 4.0ppm.
  4. In the next 7 to 10 days, keep adding the same amount of ammonia and test the parameter daily. After the 10th day, the nitrifying bacteria (AOB) should have started living in the system and breaking down ammonia into nitrite. Hence, when you’re doing your daily parameter checks, also test the nitrite levels in your system.
  5. If the ammonia concentration has dropped to 0.5ppm or 0.2ppm, add more ammonia to keep the bacteria well-fed. Therefore, refer to the amount of ammonia you’ve added to the system daily and add about three-quarters of it to prevent the bacteria from starving. Also, keep monitoring the ammonia and nitrite levels and add the ammonia if its concentration drops again (below 0.5ppm).
  6. After about 20 days, the nitrite levels will increase steadily and peak, while the ammonia concentration will reduce. This indicates that cycling has picked off, and the AOB has converted all the ammonia to nitrite. Moreover, after another 10-15 days, the nitrite levels will start declining.
  7. When this happens for a couple of days, start testing for nitrates, as the NOB have started inhabiting the system. Hence, both ammonia and nitrite levels will be approaching zero while the nitrate concentration increases (5.0-10ppm). Therefore, this portrays that the cycling process is almost complete, and you can start adding fish and plants to your system.

Here’s a YouTube video that elaborates fishless cycling in great detail:

3. Add Plants and Fish to the System

It’s safe to add fish and plants to your system when the ammonia and nitrite levels are below 0.5ppm, and the nitrate level is above 5.0ppm. However, some Aquaponic farmers prefer to introduce plant seedlings earlier before cycling is complete to allow for the development of the root system. If you do this, though, the plants may experience nutrient deficiency as the nitrate levels aren’t sufficient to nourish crops at this stage.

If you’ve chosen to introduce your plants to the system before cycling is complete, add an organic fertilizer in the grow bed. But ensure that you test the pH levels first to prevent a nutrient lockout. Preferable fertilizer sources include seaweed and compost tea.

Now, before adding your fish (or more fish if you were fish-cycling) to the system, test all the parameters, ensuring that ammonia and nitrite levels are below 0.5ppm. Another factor to consider will be the stocking density, as your system needs to be balanced. Therefore, the number of fish you’ll introduce should produce enough waste to sustain the plant volume in the unit.

If you’ve been using the fishless cycling option, it’s advisable to add a few fish at a time to the system. Therefore, add around 500 g (1.1 lb) of fish per 1000 L (264.17 gal) to avoid the upsurge of ammonia and nitrite concentrations. You can also acclimatize the fish before you introduce them to the unit.

Striking a balance in an Aquaponic system can be an uphill task as the nutrient circulation can be determined by other factors, including the biofilter size and the type of fish diet you’ll use. Therefore, you can use a fish feed rate ratio to determine the amount of feed to introduce into the system. However, it’s advisable to monitor the balance of both macro-and micronutrients in the system.

4. Speed Up the Cycling Process

Sometimes, the cycling process can take too long, depending on some factors. The bacterial colony could have slower feeding and reproduction rates in such cases. Therefore, if the system takes longer than expected, you can speed it up to complete the nitrogen cycle.

Here are several ways of speeding a cycling process:

  • Use warm water. Most nitrifying bacteria species thrive in warm water. Hence, if you’re cycling during a cold season, heat the water in your system first.
  • Use a bacterial ‘seed.’ If there’s another established Aquaponic system within your locality, borrow a part of the colony. Hence, you can obtain a part of the sludge from the grow media or some of the biofilter.
  • Use commercial bacteria. If there isn’t an established Aquaponic unit near you, get some live bacteria from your local aquarium store. The product shortens the cycling duration due to the already established bacterial colony.
  • Increase your system’s oxygen supply. Nitrifying bacteria prefer oxygen-rich environments. So, ensure that your system is well aerated before the cycling process begins. The presence of oxygen will speed up the cycle as the bacteria use it to convert ammonia to nitrites and nitrates.
  • Avoid cycling mistakes. Your system will slow down or even collapse when you throw caution to the wind or do the wrong thing. For instance, don’t use two ammonia sources simultaneously, as the ammonia will reach toxic levels. Also, avoid overfeeding your fish (if using fish cycling) during the first few days because the ammonia concentration will spike.

Note: Even after the cycling process is over, you need to monitor your system regularly. Moreover, an Aquaponic unit requires maintenance, so always keep it clean and in good shape.


Cycling is a vital phase during the establishment of an Aquaponic system. Moreover, the addition of ammonia to the unit attracts nitrifying bacteria that enable nitrification. Hence, the bacteria help maintain the symbiotic relationship between the fish and plants.

Alexander Picot

Alexander Picot is the principal creator of, a website dedicated to gardening tips. Inspired by his mother’s love of gardening, Alex has a passion for taking care of plants and turning backyards into feel-good places and loves to share his experience with the rest of the world.

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