How To Filter Water in Aquaponics (Ultimate Guide)

Depending on the type of aquaponic system you have, a filter can be one of the most crucial elements you’ll want to incorporate to ensure optimal performance and longevity. Waste can sometimes accumulate very quickly, and if poorly managed, the entire system can fail. For those wanting to maintain theirs as best as they can, this guide will take you through everything you need to know about filtering in an aquaponic system.

Here is how you can filter water in aquaponics:

  1. Understand the different types of filters
  2. Use worms and a 12-inch (30.48-cm) grow bed.
  3. Match settleable solids to the right separator.
  4. Use bird netting for suspended solids
  5. Opt for a screen filter.
  6. Feed your fish properly.

In this article, I’ll further expand into each of these steps to help you better understand and care for you aquaponic system.

1. Understand the Different Types of Filters

The first thing you’ll want to do before filtering your aquaponic system is to learn about the different types of filtration you can use. I’ll delve into some more practical steps later on, but having a proper understanding of the underlying principles will make your aquaponic maintenance experience a lot easier.

Filtration is extremely important in your system. It keeps the water clean, which in turn increases the overall health of your system’s biological life, and this increases productivity. However, there are two different types of filters you’ll want to look out for, as they’re not created equally. 


The biofilter is usually the most important filtration setup you’ll come across in aquaponics. Aquaponics is a system that relies on the symbiosis between a hydroponic and aquaculture system. 

Although each system provides what the other needs, the bridge between the two is a biofilter. A biofilter refers to a group of microorganisms cultured specifically to promote the conversion of waste from toxic ammonia to usable nitrates for plants. 

The ammonia is generally created from fish waste. However, the substance is toxic to plants as they cannot use the nitrogen contained in tits compounds. As a result, this waste passes from the tank to a separate area where the biofilter is kept. 

The biofilter then converts the ammonia into waste for usable nitrates, which are then passed on to plants. This dependence of both sides creates the symbiotic cycle that aquaponics is based on.

Because of this, the biofilter is essential to any aquaponic system. 

Here are the steps involved in preparing your home-made biofilter:

  1. Gather a bucket, two short pipes, a mesh, and expanded clay. These are all the elements you’ll need to make a functional biofilter.
  2. Make two holes in the bucket. One hole should be close to the top and will serve as the water inlet for water coming from the fish tank. The other will be at the bottom and will be the outlet for water going to your plants. Additionally, the holes should be large enough to allow the pipes to fit in.
  3. Attach a pipe to each hole. The pipes here will allow water to pass in and out of the ‘biofilter,’ connecting it to the rest of the system.
  4. Place the clay at the bottom of the bucket. The clay will provide a surface area for bacterial production and optimize their growth.
  5. Attach the mesh to the pipes to filter large particles. This step will stop your biofilter media from getting clogged with solid waste. Excessive solid waste will create ‘aerobic zones,’ which can reduce the efficiency of your biofilter and endanger the entire system.

Alternatively, you can buy a ready-made filter at your aquarium shop or online if you don’t want to make your own.

There is some misconception about the necessity of a biofilter in aquaponics. Some people say that a biofilter is not necessary. While this is partly true, there is some nuance to the answer. 

A separate biofilter is not always necessary. However, for an aquaponic system to work, there must always be some form of biofiltration. This condition means that while there might not always be an external biofilter, the process will happen regardless.

For example, if you use a media-filled system where the media provides the surface area required for the bacteria, then the media acts as the biofilter. This provision means that just because there’s no specially dedicated biofilter in the system doesn’t mean that there isn’t a biofilter at all.

Mechanical Filter

While the biofilter works at converting toxic ammonia into a usable form, the mechanical filter essentially does the same job as a traditional filter. As I mentioned earlier, the biofilter cannot do its job properly if it gets too clogged up with solid waste.

This solid waste creates aerobic zones on the media that reduce the available surface area for filtration. This drop in surface area reduces the overall system efficiency and increases the amount of ammonia that gets past the biofilter. If the ammonia levels throughout the system get high enough, they could threaten the health of both the plants and fish

Due to this, a mechanical filter is added to filter out large solid particles before they get to the biofilter. The mechanical filter can be small and functional like the mesh mentioned in the previous section, or it can be an entirely separate piece of equipment.

2. Use Worms and a 12-Inch (30.48-cm) Grow Bed

Now that you understand how filters and biofiltration work, the next step is to decide if you need a separate filter for your setup. As I previously mentioned biofilters are always present, but it’s not always necessary to set up a specialized biofilter. 

For instance, if you’re using a media-filled bed, you likely won’t need to set up a separate specialized biofilter. Media-filled systems are a type of aquaponic system where you grow your plants in grow beds filled with media. Popular options for media include gravel and expanded clay.

The most important factor you’ll need to know about media is that it has a significant surface area and is distributed throughout the bed. This extensive surface area is why you don’t need a specialized biofilter. 

In place of a biofilter, the surface of the media hosts the nitrifying bacteria. Because there is a large amount of media in the bed, bacterial growth is highly promoted.

However, if you want the grow bed to filter optimally, it is important to ensure that the bed and media are properly set out.

Here are two things you’ll want to do to properly filter a media-filled bed system:

  • Make sure your grow bed is at least 12 inches (30.48cm) deep.
  • Match your fish density to your grow bed size.

Both of these tips help your filtration in different ways. Giving your bed at least 12 inches (30.48 cm) of depth gives room for plant roots, soil bacteria, and composting worms to coexist. 

The composting worms are especially important here as they are primarily responsible for breaking down solid waste. This solid fish waste moves from the topsoil to the middle layer where the worms are. The worms, in turn, break down these solids by over half of their initial volume, releasing beneficial nutrients to the soil in the process. 

The entirety of this breakdown only begins to be optimized at around 12 inches (30.48 cm) of growth depth. Anything lower than this depth is usually not deep enough for the soil to have adequate coverage and be deep enough for an optimal worm population.

Density is also equally important if you want to keep the filtration system at optimal performance levels. While the worms and grow bed media keep the filtration system going, it’s also important to manage your fish density so that your system is not overworked.

The density I am talking about here is the ratio of your total fish weight to your growing area [Total weight(Ibs)/Grow area(ft²)]. It’s also important to make sure you don’t mix this up with stocking density which is the total number of fish/ tank size, as both ratios serve different purposes.

Generally, the optimal density you want is 1. This density ensures that the bed utilizes as much space as possible to convert waste and does not get overburdened.

Combining this density and a 12-inch (30.48-cm) depth ensures that your grow bed will filter water optimally.

Schematic diagram of a media-filled (flood and drain) aquaponic system

3. Match Settleable Solids to the Right Separator

There are different types of solid waste, and you must treat them all differently if you want to filter them properly. The first type of solids is settleable solids. They are called this because they fall to the bottom of the mixture or “set” when left alone. To remove this type of solid waste, you use a separator.

With smaller systems, you might not need one, but once your system starts to get larger, especially if you’re producing commercially, a separate filter or separator is almost always necessary.

Separators and filters work to fulfill the same purpose, but the difference in naming them comes from how they carry out their duties. Filters use material or screen to remove solids from a mixture. However, separators use techniques like density and gravity to separate solids.

Not all separators are equally efficient, and understanding the qualities of each specific type will give you a clearer idea of what you’ll need. 

Here are the three main categories of mechanical filters:

Swirl Separator

A swirl separator works based on the principle of centrifugation. Centrifugation is a separation method where denser materials in a mixture are separated using centrifugal force. 

With a swirl separator, water from the fish tank is passed into the separator. The latter is shaped so that the water is forced to swirl or spiral to the outlet. This spiral sets up a weak centrifugal force that separates solid waste from the rest of the water. 

Swirl separators are best if your system is on the smaller side, as they generally aren’t able to generate enough centrifugal force to separate the waste in a larger system.


A clarifier is a slightly more efficient option than a swirl separator. It is suitable for larger systems, but while a swirl separator works based on time, a clarifier separates waste from the rest of the water through sedimentation.

Settleable solids in a mixture will usually separate once the mixture is left to rest for a while. The solids settle at the bottom, creating a uniform layer of sludge at the bottom of the separator.

The clarifier has a divider that splits it into two parts. As the inlet and outlet are on opposing sides of this divider, water that leaves through the outlet will have gone through sedimentation, allowing it to come out almost completely clear. 

When using a clarifier, it’s important to moderate the water flow rate out of the tank. For it to be effective, the flow rate must be set so that the retention time (amount of time water stays in the clarifier before leaving) is at least twenty minutes. 

A lower retention time is not high enough for the waste to properly sediment.

Radial Flow Separator

Although it is more thorough than a clarifier, a radial flow separator also works using sedimentation techniques. The key difference between the two is how they operate.

While they both use time to separate solids from the mixture, a radial flow separator also uses changes in water velocity. 

First, the inlet of the separator is at the bottom. The water moves upwards through a pipe at the center, drastically reducing the inlet velocity because it moves against gravity.

Next, the water comes out of the top of the inlet onto a wide plate called the collection through. The conversion from translational (forwards in a pipe) to radial motion (in different directions on a plate) reduces the overall speed of the water. 

This change in velocity combined with the structure of the separator causes solids to separate from the mixture, leaving behind only clean water that later travels to the plants.

Schematic diagram of a DWC aquaponic system with a radial flow filter and biofilter

4. Use Bird Netting for Suspended Solids

Suspended solids are the second types of solids to take note of. Unlike settleable solids, they don’t settle when the mixture is left to stand because they have a density similar to water.

As a result, the previously mentioned steps are not as effective. One trusted method of separating suspended solids is to use bird netting to filter them out.

Bird netting is usually used to protect crops or fish from bird attacks. However, it can also serve to accomplish the separation purpose of filtration if the mesh is fine enough. 

To use bed netting, simply lay the net across an inlet to allow water to pass through it. As the water moves through the mesh, it leaves too large solids on top of it, and the clean water moves on to the next section.

Bird nets are best for large aquaponics systems where there is a lot of water to filter. The only major downside to using bed netting is the cleanup. The suspended solids cling to the netting, and it is important to take the net down and clean off the waste periodically.

5. Opt for a Screen Filter

A screen filter functions similarly to bird netting and is a very good way to filter out suspended solids. The key difference between the two lies in the type of material used for filtration.

Screen filtration doesn’t use nets. Instead, it uses porous materials like muslin to strain the water and separate the solid waste. The advantage of screen filters is that the mesh is a lot finer and, as a result, will catch a far smaller waste than bird netting will.

6. Feed Your Fish Properly

This tip is more of a preventative approach rather than a cure; however, it’s no less important in terms of water quality. As important as it is to feed your fish to keep them alive, it is equally important to make sure you’re feeding them the right way too.

Doing so involves far more than just regular feeding. It also incorporates a variety of practices that although may seem overly complicated at first, can make a notable improvement to the quality of your system.

Here are some tips to follow to make sure you’re feeding your fish the right way:

  • Do not overfeed your fish. Overfeeding your fish leaves them with far more food than they need. Having this much food causes problems with water quality and excess fish waste. The right amount to feed fish is about 2% of their body weight each day. You can take this as 2% of the total weight of fish you’re producing while adding a little leeway for error.
  • Do not suddenly change your fish diet. What you feed your fish is almost as important as how much you feed them. Different types of fish respond differently to different types of feed. As a result, changing your feeding brand suddenly can mean that many of the species won’t  be able to eat the same volume they have been. 

To avoid this when changing brands, test a small amount over a few days and see how the fish react before changing their diet entirely.

  • Keep your fish in optimal conditions. It is extremely important to ensure that your fish stay in the best conditions, so they respond as well as possible to feeding. Temperature, pH, oxygen, and everything other environmental factor should be as optimal as possible. Conditions too far off from ideal will stress your fish and stressed fish eat significantly less.

Do You Need a Filter In an Aquaponic System?

The main draw of an aquaponic system is the fact that it’s supposed to be a symbiotic and self-running environment, so, understandably, many people may feel a filter is unnecessary. However, some some enthusiast heavily oppose these opinions and believe having a dedicated filter greatly improves the quality and longevity of a system. Both sides present valid arguments, but which is right?

You do not need a filter for most aquaponic systems. Most systems are small-scale or backyard varieties and, as a result, can filter themselves fine without a specialized device. However, a filter can be necessary for larger systems if you want to keep an optimal water condition.

A smaller system, like a media system, usually does not need a dedicated filter. The surface area of the media is usually enough to keep things running at close to optimal conditions. However, for larger models like NFT and raft systems, it can sometimes be necessary to have filters in place.

This situation is especially true for NFT systems as things can get very dirty quickly. Since they use a channel, the amount of space and time the water has to move is usually very low. Because of this, clogging of the pipes can easily become a serious issue, and I would advise you to use a filter with most NFT systems.

Why Do You Need a Filter In an Aquaponic System?

You need a filter in an aquaponic system to maintain optimal water quality. Water filters will optimize a system’s quality by filtering out excess waste before it accumulates. This reduces the pressure put on your biofilter and makes it easier for your plants to absorb nutrients.

Both types of filters are extremely important. For example, biofilters do important work by converting nitrogen compounds to a form where it is usable by the plants. This conversion keeps the system running optimally, and your plants stay in good health for a healthy harvest. 

On the other hand, mechanical filters filter out solids in the water. The benefits of this process are multi-faceted:

  • They prevent clogging. In aquaponics, like in all other forms of aquaculture, your pipes can easily get clogged from waste, excess feed, or external factors. Having a mechanical filter in place can save you from the hassle of unclogging your pipes.
  • They reduce the load on the biofilter. When solids get into your biofilter and stay there long enough, they can reduce the surface area available for the biofilter to convert nitrogen compounds. A mechanical filter stops this by preventing those solids from reaching the biofilter in the first place.
  • They keep your system cleaner. Filtering waste with a specialized equipment will keep your  system looking better by reducing water turbidity.

A filter might not always be a necessity; however, having one will rarely ever be detrimental. Because of this, I advise most people to get one if they can spring for it. It’s better to have a high-quality filtration system and not need it than to need it and not have it at all.

Final Thoughts

Hopefully, this guide has helped a great deal with your filtration problems. Getting filtration right is one of the most crucial elements you’ll want to consider when maintaining an aquaponic system, and once done properly, your overall productivity can greatly increase.

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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