The Role of Biofilters in Aquaponics Systems

One important aspect of aquaponics systems is the maintenance of water quality, as this directly impacts the health and productivity of both fish and plants. Aquaponics systems operate on the symbiotic relationship between fish and plants. 

Fish waste which is rich in nutrients serves as a natural fertilizer for plants. In return, the plants filter and purify the water, creating a pristine environment for the fish. However, maintaining optimal water quality is essential to ensure the success and sustainability of these systems.

This is where biofilters come into play. Biofilters play a vital role in aquaponics systems by removing harmful substances and transforming them into less toxic forms. These filters house the beneficial bacteria that perform nitrification, which converts toxic ammonia produced by fish waste into nitrate. 

Additionally, biofilters remove solid waste and other organic matter, preventing their accumulation in the system. By facilitating the biological breakdown of waste and pollutants, biofilters ensure a healthy and balanced environment for fish and plants in aquaponics systems.

This article, will discuss the roles of biofilters in aquaponics systems. We will also delve into different types of biofilter systems commonly used in aquaponics and provide troubleshooting tips to ensure their proper functioning. 

Understanding the Use of Biofilter in Aquaponics Systems

Understanding the role and significance of biofilters is essential for aquaponics enthusiasts and growers. Aquaponics systems can achieve optimal water quality by implementing efficient biofilter systems, leading to improved fish health, robust plant growth, and increased overall system stability. Moreover, biofilters reduce water consumption and aquaponics' sustainability as a viable agricultural practice.

What is Aquaponics Biofilter?

Biofilters are essential components of aquaponics systems designed to maintain water quality. They are specifically engineered to foster the growth of beneficial bacteria that play a crucial role in the nitrogen cycle. These bacteria convert harmful ammonia, generated by fish waste and uneaten fish food, into nitrate, a form of nitrogen that is a valuable plant nutrient.

DIY aquaponics Biofilter

How Biofilters Work to Maintain Water Quality 

Biofilters employ physical, chemical, and biological processes to maintain optimal water quality in aquaponics systems. These filters typically contain bio media that serves as a habitat for the beneficial bacteria. As water containing fish waste and uneaten food passes through the biofilter, these bacteria adhere to the surface of the filter media and help convert ammonia into nitrates or nutrients for the plants. Biofilters also play a role in removing solid waste and organic matter from the water. The filter media provides a physical barrier, capturing particulate matter and preventing its accumulation in the system. 

The Different Types of Biofilters Used in Aquaponics Systems 

Various types of biofilters are employed in aquaponics systems, each with its advantages and considerations. Some three common types of biofilters used in aquaponics systems are: 

1. Moving Bed Filter

A moving bed consists of a container or tank filled with small plastic media that move and circulate with water flow. The plastic media used in a moving bed filter are typically small, lightweight pieces with a high surface area. This surface area provides a substrate for beneficial bacteria to grow and colonize. These bacteria form a biofilm on the media's surface, where they break down and convert harmful ammonia and nitrite compounds into less toxic nitrate.

The unique aspect of a moving bed filter is that the plastic media are constantly in motion. This movement is typically achieved using air or water flow within the filter. The continuous motion ensures that the biofilm on the media is constantly exposed to oxygen and nutrients, optimizing the bacterial activity and efficiency of the filter.

As water flows through the moving bed filter, the bacteria on the media metabolize the ammonia and nitrite, effectively removing these harmful compounds from the water. The filtered water then continues to other parts of the aquaponics system.

Moving bed filters are popular in aquaponics systems because of their compact design, high surface area for bacterial colonization, and efficient ammonia and nitrite removal. 

2. Drip Filter

A drip filter involves using a drip irrigation system that delivers water to the plant-growing area in a controlled manner. It consists of a container or tank filled with solid filter media, such as foam pads, filter mats, or other porous materials. The water from the aquaponics system is directed into this container, where it trickles down through the filter media.

As the water drips through the filter media, it undergoes mechanical filtration, capturing and removing larger particles and solid waste. The filter media act as a physical barrier, preventing these particles from entering the plant-growing area.

The filtered water then drips out of the filter container and is directed to the plant roots for nutrient uptake. This controlled irrigation method ensures the plants receive the necessary water and nutrients while maintaining a clean and filtered water supply.

3. Static Filter

A static filter is a biofilter that provides mechanical and biological filtration without moving parts. It is a stationary filter designed to remove solid waste particles and facilitate the growth of beneficial bacteria.

A static filter typically consists of a container or chamber filled with filter media, such as foam pads, filter mats, or other porous materials. The water from the aquaponics system flows into the filter, where it passes through the media. As the water flows through the static filter, the filter media trap and removes solid waste particles suspended in the water. This process is known as mechanical filtration, as it physically separates the larger particles from the water.

The filter media provides a large surface area for beneficial bacteria to grow and colonize. These bacteria perform biological filtration by converting harmful compounds like ammonia and nitrite, produced by fish waste, into less toxic nitrate. The static filter supports establishing a healthy bacterial population, which contributes to maintaining water quality and nutrient balance in the system.

Depending on the system design, The filtered water exits the static filter and continues to other parts of the aquaponics system, such as the plant growing area or fish tank.

Static filters are popular in aquaponics due to their simplicity, low maintenance requirements, and effective filtration capabilities. They help remove solid waste and promote the growth of beneficial bacteria, ensuring a clean and healthy environment for both plants and fish.

The Role of Biofilters in Aquaponics Systems

1. Conversion of Fish Waste Into Plant Nutrients

One of the primary functions of biofilters in aquaponics systems is to convert fish waste into plant nutrients. Fish excrete waste, which contains ammoniaand other nitrogenous compounds. If left unprocessed, these compounds can accumulate and become toxic to fish.

The beneficial bacteria break down the fish waste within the biofilter and convert it into forms that plants can readily absorb. The biofilter acts as a mediator in transforming fish waste into nutrient-rich water continuously delivered to the plants.

Aquaponics systems establish a closed-loop system where waste is recycled, and resource utilization is maximized by utilizing biofilters to convert fish waste into plant nutrients. This benefits plant growth and reduces the need for external fertilizers, making aquaponics an environmentally friendly and sustainable farming method.

2. Removal of Solid Waste and Organic Matter

Biofilters also contribute to removing solid waste and organic matter from the aquaponics system. As water flows through the biofilter, the filter mediaor substrate acts as a physical barrier, capturing and trapping particulate matter, uneaten food, and fish waste.

By removing solid waste and organic matter, biofilters help maintain water clarity and prevent the release of harmful substances into the aquaponics system. This contributes to the overall cleanliness and health of the system.

3. The Role of Biofilters in Water Filtration

Biofilters play an essential role in maintaining water quality within aquaponics systems. As the water circulates through the biofilter, it undergoes a natural filtration process which helps remove impurities and ensures a healthy environment for fish and plants. This filtration is achieved through the actions of beneficial bacteria and microorganisms that colonize the biofilter. The biological filtration process effectively removes pollutants and promotes water clarity, creating an optimal environment for aquatic life.

4. Enhanced Nutrient Cycling and Plant Growth

Biofilters play a vital role in the nutrient cycling process within aquaponics systems. The conversion of ammonia into nitrate by beneficial bacteria provides a consistent supply of nutrients to plants. Nitrate serves as a valuable source of nitrogen, promoting robust plant growth, improved yields, and enhanced nutritional value. By efficiently recycling nutrients, biofilters contribute to the sustainable and efficient use of resources in aquaponics and allow plants to thrive without the use of external fertilizers.

5. Increased System Stability and Resilience

Biofilters play a crucial role in maintaining system stability and resilience in aquaponics. The presence of beneficial bacteria in the biofilter creates a balanced microbial community that contributes to the overall stability of the ecosystem. These bacteria help establish a robust biological filtration system that efficiently converts toxic substances like ammonia into less harmful forms. This biological balance enhances the system's resilience by preventing rapid fluctuations in water quality, ensuring a stable environment for fish and plants. 

Factors to Consider in Using Biofilter in Aquaponics Systems

When using biofilters for aquaponics, several factors should be taken into consideration. Considering these factors will help ensure that the biofilter functions effectively and contribute to the overall success of the aquaponics system.

  1. System Size and Stocking Density: The size of the aquaponics system and the number of fish and plants it can support will determine the size and capacity of the biofilter.
  2. Media Selection and Sizing: Choosing the appropriate media for the biofilter is crucial. Also consider factors such as porosity, surface area, and durability. The media should also be sized correctly to ensure proper water flow and prevent clogging.
  3. Water Flow and Oxygenation: Adequate water flow is necessary to ensure uniform water distribution throughout the biofilter and promote efficient filtration. Oxygenation is essential to support the growth of beneficial bacteria and maintain aerobic conditions.
  4. Nutrient Balance: Maintaining a balance between fish and plant biomass is crucial. Overstocking the system can overload the biofilter and affect its performance. It is essential to ensure that the biofilter can effectively process the waste produced by the fish.
  5. Maintenance and Monitoring: Regular maintenance tasks, such as cleaning the biofilter media, monitoring water parameters, and inspecting equipment, should be carried out to ensure the optimal functioning of the biofilter.
  6. pH and Temperature: The pH and temperature of the watercan affect the activity of beneficial bacteria in the biofilter. Monitoring and maintaining suitable pH and temperature ranges are essential for their growth and efficiency.
  7. System Design and Integration: The biofilter should be integrated properly into the aquaponics system design, and factors such as water flow, plumbing, and space availability should be considered.

Is Biofilter Required in All Aquaponics Systems?

No, a biofilter is not always required in all aquaponics systems. The need for a biofilter depends on the specific design and setup of the aquaponics system. There are different aquaponics systems, and some may utilize alternative methods for water filtration and nutrient management.

While biofilters are commonly used and highly effective in most aquaponics systems, specific setups, such as the media based, may not require an additional biofilter. This is because the grow media provides enough surface area for the bacteria to live and acts as a biofilter. However, you should still provide the right environment, such as pH control and proper aeration, for the bacteria to thrive. 

Ultimately, the decision to include a biofilter or add alternative filtration methods depends on the aquaponics system's specific requirements, preferences, and goals and the aquaponic grower.


Biofilters play an important role in the success of aquaponics systems. They contribute to maintaining water quality, promoting fish health, and enhancing plant growth. By understanding their role, implementing effective designs, and addressing issues proactively, you can create thriving and sustainable systems that maximize the productivity of both fish and plants. 

Frequently Asked Questions

1. What are the benefits of using biofilter in aquaponics?

Using a biofilter in aquaponics has several benefits, these include:

  • A biofilter helps maintain the optimal water quality for the health of fish and plants.
  • It helps promote the growth of beneficial bacteria is essential for nitrification.
  • It aids in converting fish waste into valuable nutrients for plants.
  • It helps create a self-sustaining ecosystem that minimizes the need for external inputs.
  • Supporting healthy plant growth and maximizing productivity.

2. Do I need a biofilter if I have a small aquaponics system?

Yes, even in small aquaponics systems, a biofilter is essential. It helps maintain water quality, removes toxic compounds, and converts fish waste into nutrients. A properly sized and designed biofilter ensures a balanced ecosystem, supporting the health and growth of both fish and plants.

3. How often should I clean and maintain the biofilter?

The frequency of cleaning and maintenance depends on various factors such as system size, stocking density, and water quality. Generally, biofilters require periodic maintenance, including cleaning media, checking water flow, and monitoring parameters. Establishing a regular maintenance routine is recommended based on your aquaponics system's specific needs.

4. Can I use different types of media in the biofilter?

Yes, different media types can be used in the biofilter, such as gravel, expanded clay, lava rock, or biofilter-specific media. The choice of media depends on factors like porosity, durability, and its ability to provide a suitable environment for bacterial colonization.

5. What happens if the biofilter fails or malfunctions?

If the biofilter fails or malfunctions, the water quality in the aquaponics system can deteriorate rapidly. Toxic compounds like ammonia and nitrite may increase, posing a risk to the health of fish and plants. Regularly monitoring and maintaining the biofilter help prevent such failures and ensure a well-functioning system.

3 Responses



July 27, 2021


Wm David Wilhelm

Wm David Wilhelm

July 27, 2021

In addition to a Bio media filters for fish outlets, I am considering using a Bio media pre-filter for all returns from plant media beds for fine particulate accumulation and additional mineralization with airlift and higher O2 levels for fish. If it all works, as designed and will reduce the addition of nutrient top off and JAW (just add water) is the goal and best wishes to all. Hint, hint, Catfish for any Crayfish that get loose from the system floating mats, vertical racks primers for faster nutrient uptake crops and cleaner clearer water. Circularize your plant media beds for less stagnation and anaerobic activity, by spiralizing the water flow.

Daniel Schneekloth

Daniel Schneekloth

July 27, 2021

I know my question is not gonna be a black or white answer as it probably depends on water quality and other factors too. But is there a volume of water flow rate per amount of surface area of your bio filter? Just using random numbers as example. Say 50 gallons a minute for 5000 square feet of surface area?

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