How to Cycle New Aquaponics Systems

By harnessing the natural relationship between aquatic life and plants, aquaponics systems offer a holistic approach to agriculture, where fish waste provides essential nutrients for plant growth, while plants filter and purify the water for the aquatic organisms. However, the successful establishment operation of an aquaponics system depends on a critical process known as cycling.

Cycling, refers to the establishment of beneficial bacteria within the system that convert harmful ammonia from fish waste into nitrites and then into nitrates, which serve as vital nutrients for plant growth. Essentially, cycling initiates the biological filtration process that ensures water quality and sustains the ecosystem's balance.

In this blog, we will discuss the various methods of cycling new aquaponics systems, and explore their techniques, benefits, and considerations to guide aspiring aquaponics enthusiasts towards a successful start of their own aquaponics system.

What is System Cycling?

Cycling in aquaponics refers to the process of establishing and maturing the necessary microbial populations within the system to efficiently convert toxic compounds, such as ammonia and nitrites, into less harmful forms, particularly nitrates. This process is essential for creating a stable and balanced ecosystem where fish and plants can thrive.

The purpose of cycling: The primary purpose of cycling in aquaponics is to establish a robust microbial community, particularly beneficial bacteria, that play a vital role in maintaining water quality. These bacteria facilitate the conversion of toxic ammonia, primarily produced by fish waste, into nitrites and then into nitrates, which serve as essential nutrients for plant growth. Cycling kick-starts the biological filtration process, ensuring that the aquaponics system can effectively remove harmful substances from the water, promoting the health and well-being of both fish and plants.

New Aquaponics System

The Importance of Establishing Beneficial Bacteria in Aquaponics Systems 

The establishment of beneficial bacteria is important for several reasons:

  1. Beneficial bacteria play a key role in converting toxic ammonia into nitrites through a process called nitrification. This conversion helps prevent ammonia toxicity, which can be harmful or even fatal to fish.
  2. Another group of beneficial bacteria further convert nitrites, which are also toxic to fish, into nitrates. This step completes the nitrogen cycle, making the nitrates available as nutrients for plants.
  3. By converting ammonia and nitrites into nitrates the beneficial bacteria facilitate the recycling of nutrients within the aquaponics system
  4. Establishing beneficial bacteria helps stabilize the aquaponics system by maintaining consistent water quality parameters. This stability is essential for minimizing stress on fish and plants, reducing the risk of disease outbreaks, and promoting overall system resilience.

How to Cycle New Aquaponics Systems

A. Fishless Cycling

Fishless cycling involves cycling the aquaponics system without the presence of fish initially. Instead, a source of ammonia, such as household ammonia or fish food, is used to simulate the waste produced by fish. This allows beneficial bacteria to establish and multiply without subjecting fish to potentially harmful ammonia spikes.

Pros and cons:

  • Pros: Fishless cycling reduces stress on fish, minimizes the risk of fish loss due to ammonia toxicity, and allows for precise control over the cycling process.
  • Cons: It requires patience as it typically takes longer than fish-in cycling. Additionally, without fish waste, some argue that the bacteria may not fully adapt to the specific conditions of the system.

Steps involved in fishless cycling:

  1. Preparing the System: Fill the fish tank with water and add any necessary dechlorinator to remove chlorine and chloramine, which can harm beneficial bacteria.
  2. Adding Ammonia Source: Introduce the ammonia source, such as household ammonia or fish food, to the system to create an ammonia concentration of around 2-4 ppm (parts per million).
  3. Monitoring Ammonia and Nitrite Levels: Regularly test the water parameters, including ammonia and nitrite levels, using appropriate test kits. As the beneficial bacteria colonize, they will begin converting ammonia into nitrites.
  4. Wait for Nitrite Spike: After a period of time, typically 2-6 weeks, a spike in nitrite levels will occur as the bacteria responsible for converting nitrites into nitrates establish themselves.
  5. Testing for Nitrate: Once nitrites begin to decline, test for nitrates, which indicate that the cycling process is nearing completion.
  6. Completing Cycling: Once ammonia and nitrite levels consistently read zero and nitrates are present, the system is cycled and ready for the introduction of fish.

B. Cycling with Fish

Cycling with fish involves cycling the aquaponics system with fish present from the beginning. The fish produce ammonia as waste, which kick-starts the cycling process by providing the necessary ammonia source for beneficial bacteria colonization.

Pros and cons:

  • Pros: Fish-in cycling more closely simulates the natural ecosystem and may result in faster cycling compared to fishless methods. It also allows for immediate stocking of fish, reducing the overall cycling time.
  • Cons: There is a higher risk of fish stress or loss due to exposure to elevated levels of ammonia and nitrites during the cycling process. It requires careful monitoring and may necessitate water changes or other interventions to protect fish health.

Steps involved in fish-in cycling:

  1. Preparing the System: Similar to fishless cycling, prepare the system by filling the fish tank with water and adding any necessary dechlorinator.
  2. Introducing Fish: Add fish to the system at a stocking density appropriate for cycling, typically lower than the final stocking density to reduce ammonia levels.
  3. Monitoring Water Parameters: Regularly test water parameters, including ammonia, nitrite, and nitrate levels, to track the progress of cycling and ensure fish health.
  4. Observing Ammonia and Nitrite Spikes: As the beneficial bacteria colonize, monitor for spikes in ammonia and nitrite levels, which indicate the establishment of the nitrogen cycle.
  5. Completing Cycling: Once ammonia and nitrite levels consistently read zero and nitrates are present, the cycling process is complete, and the system is ready for full stocking.

C. Seeding from Established Systems

Seeding involves inoculating a new aquaponics system with beneficial bacteria obtained from an established and healthy aquaponics system. This method accelerates the cycling process by introducing a mature microbial community that can rapidly colonize the new system.

Pros and cons:

  • Pros: Seeding from established systems can significantly shorten the cycling period, sometimes to just a few days, by introducing a mature microbial community. It reduces the risk of ammonia and nitrite spikes and promotes a more stable ecosystem from the outset.
  • Cons: It requires access to an established aquaponics system for obtaining the beneficial bacteria. There is also a risk of introducing pathogens or undesirable organisms along with the beneficial bacteria, although this can be mitigated through careful selection of the source system and thorough sanitation procedures.

How to collect beneficial bacteria from established systems:

  1. Identify a well-established aquaponics system with stable water parameters and healthy fish and plants.
  2. Obtain a sample of biofilm or grow media from the source system, which contains a high concentration of beneficial bacteria.
  3. Add the collected biofilm or media to the new aquaponics system, distributing it evenly throughout the grow beds or filtration components.
Water Test in Aquaponics

Factors That Affect The Cycling Process

A. Water parameters to monitor during cycling:

1. Ammonia:

Ammonia levels should be closely monitored during cycling, as they indicate the presence of fish waste and the progress of bacterial colonization. Elevated ammonia levels can be harmful to fish and may delay or stall the cycling process. As cycling progresses, ammonia levels should decrease as beneficial bacteria convert it into nitrites and then into nitrates.

2. Nitrite:

Nitrite levels also need to be monitored, as they represent an intermediate stage in the nitrogen cycle. Nitrites are toxic to fish at high concentrations, so their presence indicates that the cycling process is underway but not yet complete. As beneficial bacteria establish themselves, nitrite levels should decline.

3. Nitrate:

Nitrate levels indicate the final stage of the nitrogen cycle and the presence of beneficial nitrifying bacteria. While nitrates are less toxic to fish than ammonia and nitrites, excessively high nitrate levels can still be detrimental. Regular monitoring ensures that nitrate levels remain within acceptable limits and do not accumulate to harmful levels.

B. Temperature considerations:

Temperature plays a crucial role in the cycling process, as it influences the activity and growth rate of beneficial bacteria. Ideally, the water temperature should be maintained within the optimal range for bacterial growth, which is typically between 20-30°C (68-86°F).

Lower temperatures can slow bacterial metabolism and prolong the cycling process, while higher temperatures can accelerate bacterial activity but may also increase the risk of fish stress or disease. Monitoring and maintaining stable water temperatures within the recommended range are essential for promoting efficient cycling and ensuring the health of fish and bacteria alike.

C. pH levels and their impact on cycling:

pH levels also affect the cycling process, as they influence the activity of nitrifying bacteria responsible for ammonia and nitrite conversion. Beneficial nitrifying bacteria thrive within a specific pH range, typically between 6.8 to 7.5, with some variations depending on the species. Outside of this optimal pH range, bacterial activity may be inhibited, leading to delays or disruptions in the cycling process.

Regular monitoring of pH levels throughout the cycling process allows for timely adjustments, such as the addition of pH buffers or water changes, to maintain optimal conditions for bacterial growth and cycling progress

Troubleshooting Common Issues During Cycling

Despite careful planning and monitoring, aquaponic systems may encounter common issues during the cycling process. Understanding and addressing these challenges promptly can help minimize disruptions and promote successful cycling. Some common issues and troubleshooting tips include:

1. Ammonia or nitrite spikes:

If ammonia or nitrite levels spike during cycling, it may indicate an imbalance in the system or insufficient beneficial bacteria to handle the waste load. To address this, perform partial water changes to dilute the concentration of toxins, reduce feeding rates to lessen the waste produced, and ensure adequate aeration to support bacterial growth. Consider extending the cycling period if necessary until ammonia and nitrite levels stabilize.

2. pH fluctuations:

Fluctuations in pH can impact bacterial activity and the health of fish and plants. To stabilize pH levels, use pH buffers or additives as needed, and avoid sudden changes in water chemistry. Regularly test and adjust pH to maintain optimal conditions for bacterial growth and cycling progress.

3. Slow cycling progress:

If cycling progress seems slow or stalls, review the system's parameters, including temperature, pH, and nutrient levels. Ensure that all components are functioning correctly, such as the filtration system and aeration, and consider providing additional sources of beneficial bacteria, such as seeding from established systems, to jump-start the process. Patience is key, as cycling may take longer under suboptimal conditions, but diligent monitoring and adjustments can help overcome challenges and promote successful cycling in the long run.


In a new aquaponics system, cycling serves as a critical foundation for success. Through the establishing the beneficial bacteria,you create a balanced and resilient ecosystem where fish and plants thrive in symbiosis. Cycling, whether through fishless methods, cycling with fish, or seeding from established systems, lays the groundwork for efficient nutrient cycling, water purification, and ecosystem stability.

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