Anyone already familiar with aquaculture knows there was a vital component missing from our breakdown of aquaculture hardware, the filtration! We’ve separated it because in aquaponics, it is more than just about filtering out the waste. In aquaponics, microbes biologically filter the water for our plants which then filter the water for the fish. We feel that the miniscule microbe deserves its due and that is why we decided to separate the filtration system apart from the aquaculture system as the second aspect of the aquaponics hardware trifecta.

The main purposes of the filtration system in aquaponics are:

  • Removing solid waste from the water.
  • Providing a thriving habitat for nitrifying bacteria to convert ammonia to nitrite to nitrate.
  • Providing a thriving habitat for heterotrophic bacteria to make mineral compounds available for the plants.
  • Polishing water to a clarity level acceptable by food safety standards.

Your fish will produce a large amount of solid waste. We are talking straight up POOP! You want this out of your system as quickly as possible, especially once you start transitioning into a commercial operation. To do this, you’ll need a carefully engineered filtration system. 

We will focus on three aspects of the filtration system. Unlike the aquaculture system and the hydroponics system, the filtration system is not contained in any single area in your aquaponics system and has a few key pieces of hardware at different locations.


Clarifier - The main mechanical filter mechanism and the first level of biological filtration in an aquaponics system. It’s main purpose is to remove solids and provide a home for denitrifying bacteria. The clarifier immediately follows the aquaculture system. Typically the clarifier flows directly into the hydroponics system, although sometimes it flows into the sump tank and from there into the hydroponics system. This all depends on your system design. 

There are two components of the clarifier system: the solids removal system and the bioremediation system. The Solids Removal System ALWAYS comes before the Bioremediation system. Don’t neglect this!

  1. The Solids Removal System (SRS) pulls solid waste out of the water column and collect them for easy removal. Our prefered method is known as a swirl filter. The primary tank is a cone bottom barrel. The circular flow will slowly collect solids out of the water column and drop them into the cone. A spigot on the tapered end of the cone releases the solid waste into a bucket. This lovely fish effluent can be prepared as high-potency fertilizer, compost, or compost tea. It is rich in a wide spectrum of nutrients and beneficial microorganisms. 
  2. The Bioremediation System (BRS) system is the fancy term for the microbes' home. BRS is done in many different ways, beyond the scope of this article, but no matter which style you chose, it all boils down to providing a large amount of surface area for microbes to live and grow. A common form of BRS that we have used many times is a simple gravity flow-through filter. In medium size systems, we use food-safe 55 gallon barrels as the main BRS tank. We use a mix of expanded shale and biochar for the biological surface area of the BRS. We’ll talk more about grow media in the next section. Water flows in and is forced through the grow media before floating onwards to its next destination.

Growing Media
We’ll talk more about growing media in the hydroponic system hardware section, but it is crucial to recognize the importance of grow media to the microbes living in your filter.

Growing media provides shelter to microbes and storage for the nutrients that microbes, as well as plants, use. We like to think of the grow media as a city for microbes. Much like humans cities provide a certain level of security and abundant resources, compared to say a nomad wandering the Sahara Desert, the grow media provides the microbes a space with guaranteed shelter and abundant stored resources. The microbes are able to proliferate and do their job extremely effectively in the biological surface area of the grow media.

Many types of grow medium exist with a variety of properties and benefits. One is worth calling out specifically here in the Filtration System section. Biochar, or agricultural charcoal, is a remarkable filter/grow media that is gaining attention for many of the miraculous properties it exhibits. Biochar’s greatest feature is its exceptionally high surface area per volume of char. Biochar exhibits microscopic and nanoscopic pores throughout the carbon matrix. Microscopic pores provide shelter for microbes and nanoscopic pores act as storehouses by actually attracting nutrient ions to them through adsorption (not absorption). Biochar is made through pyrolysis and can easily be done in a backyard or driveway on a small scale, making this wonderful substance available to anyone willing to start a little fire!

The Sump Tank
The sump tank is simply the term for the lowest portion of your system. Gravity will naturally collect water at the sump tank. There are two types: “In-line” versus “mixing” sump tanks in aquaponics systems.

In-line sump tanks immediately follow the hydroponics grow area and pump back into the fish tank. They are called in-line because this creates a unidirectional flow from aquaculture to clarifier to hydroponics to the sump, then back to the aquaculture area.

Mixing sump tanks receive water from and distribute water to the aquaculture and hydroponics areas simultaneously. They “mix” the water from the fish tank and plant beds and help create homogenous nitrogen levels across the entire system. Mixing sump tank systems can simplify plumbing, especially when height levels create issues for the unbroken flow with an in-line system.

Water pumps are most commonly installed in the sump tank. When the water pump is in the sump tank, it is possible to run an aquaponics system on a single pump because gravity will constantly return water to the sump as it is pumped out. This method is commonly referred to as CHOP (constant height, one pump) or CHIFT-PIST (constant height in fish tank, pump in sump tank). We strive to keep every aquaponics system we design down to only a single pump and we think you’ll have a better chance of success if you do too. Multiple pumps inevitably start pumping at different rates which will destroy your carefully plotted flow projections. Keep it simple and CHOP your system.

Small pumps can be found on We trust the Active Aqua and EcoPlus brands. Remember, when sizing your pumps, the flow gallons per hour (GPH) should at least equal your aquarium volume. Larger pumps are typically rated on a chart mapping their GPH versus head height, or how high the pump has to move water. Pumps lose power as they pump higher and higher, so it is very important to consider the height you have to move your water before choosing your pump. A pump’s maximum GPH correlates to a 1 foot head height. When your head increases, your GPH decreases. Reducing your plumbing size, will also reduce your GPH, while increasing the work your pump needs to do, reducing its lifespan.

Engineering for Water Quality


Oxygen is vital to the aerobic microbes in your clarifier. A rule of thumb suggested in Recirculating Aquaculture 3rd Edition is 1.0 kg oxygen per kg of feed as a starting point. This will ensure adequate oxygen for the nitrifying bacteria to fully convert the ammonia-nitrogen into nitrates. This is especially important for commercial producers with large aquaculture components. Aeration should be added within or immediately before the bioremediation aspect of the clarifier.

Flow Rates

Flow rates are important in filtration because velocity impacts the ability for solid waste to fall out of the water column. If water flows too fast, it will disturb the solids and you won’t be able to capture them. However, if you go too slowly, the fish tank will not be able to turn over the required volume per hour. A good rule of thumb is to have your clarifier total volume at one-third the total volume of your culture tanks. That sizing combined with adequate plumbing size will ensure your clarifier runs slow enough to capture solids while maintaining adequate outlet flow from the fish tank.

Plumbing Size

The best way to go about plumbing your filtration is to always err towards oversizing. The difference in pressure between a 1” pipe and a 3” pipe is tremendous. 1” will create a jet that will disturb your solids and ensure you never collect any awesome fish effluent, while a 3” pipe will ensure a gentle flow even with a higher flow rate. Of course, this is all relative, every scale system has different plumbing needs. Just remember, err towards oversizing!

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