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Aquaponics System Odor: How to Identify and Fix

Aquaponics System Odor

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Owning an aquaponics system means consistently checking up on your unit to ensure that both plants and fish are getting the required nutrients to grow. This can be done by monitoring the water quality of the fish tanks, checking plants for signs of nutrient deficiencies, or ensuring that pests aren’t taking over your grow bed. However, despite doing routine system maintenance, some units still go haywire due to preventable causes. One indicator that your system is not maintained well is if it gives out a foul smell. But how can you identify the source of aquaponics system odor? What can you do to fix it?

An aquaponics system doesn’t usually stink unless you have a bad fish waste management system in place. Aside from this, anaerobic zones such as the pipes and the grow beds should be consistently checked to lessen the sulfur smell they gave off. When neglected, these minor causes might create a system imbalance that will significantly affect the condition of your plants and fish.

To help you identify the source and fix aquaponics system odor, here is a detailed list of the three major things you have to monitor consistently.

Fish waste management system

An aquaponics unit needs an effective waste management system to minimize water pollutants and prevent pungent smell coming off from the unit. Two types of waste accumulate in the fish tank that should be addressed immediately:

Managing solid waste in aquaponics

Solid waste is commonly considered to be the most dangerous waste in a fish culture system. Aside from causing a foul smell to the fish tank, it can also kill fish by clogging their gills. Most solid waste found in an aquaponics system is from uneaten feed pellets and fecal droppings. This waste can also clog the water flow of the whole aquaponics system and might cause anoxia to the plants. To prevent this, mechanical filtration is needed.

Mechanical Solids Filtration

There are many types of mechanical filtration systems that can be installed in an aquaponics unit, but the simplest and most effective method is the clarifiers and mechanical separators. This can be done by putting a screen between the fish tank and the grow beds. The screen will filter the solid wastes, and the grower will only have to remove and rinse it from time to time to ensure its effectiveness.

Aside from clarifiers, growers may also opt to use sand filters, sedimentation tanks, and other filtration systems depending on the size of their aquaponics unit. For small scale systems, however, simple clarifiers will do.

Managing dissolved waste in aquaponics

Dissolved waste can be derived from fish waste that is too small to be removed mechanically or uneaten feed that is left to decompose in the tank. Although in both cases beneficial nutrients are released into the water to some extent, an oversaturation will affect water quality and serve as a pollutant to the fish. 

Nitrogen and phosphorus are significant components of fish feed that can increase water turbidity which is known to harm the vision of fish and increase the water temperature. On the other hand, dissolved fish waste that is not managed correctly can be harmful because it is in the form of ammonia, which is toxic to the fish and has a strong smell. To prevent these pollutants, your aquaponics system must have a biofilter installed.



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Through biofiltration, harmful substances like ammonia are converted by living bacteria into nitrates that serve as a useful nutrient for the plants. The biofilter is usually installed between the mechanical filter and the grow beds and houses an adequate amount of bacteria for better biofiltration. It also requires aeration from an air pump for the nitrifying bacteria to oxidize ammonia.

Anaerobic zones in Aquaponics

Anaerobic zones in Aquaponics

Another reason why aquaponics system odor has been a problem of some growers is due to unmanaged anaerobic zones or the parts of the system that lack oxygen. Performing regular maintenance of some pipes that might be clogged or the unoxygenated layers of the grow bed is necessary to achieve a traditional earthy garden smell. You may use air stones in that area to lessen the sulfur stench it gives off and to neutralize the smell in general.

Dead fish

Most of the time, the foul odor of an aquaponics system is due to the decay of dead fish in the tank. It is vital to follow the correct water and feeding parameters so the fish can thrive and avoid instances where they die and create a foul smell. Growers should also immediately remove dead fish to reduce health hazards to the other fish in the system.


Identifying the source of aquaponics system odor can be easy if you know where to look. One of the primary reasons why the system suddenly produces an unpleasant smell is because of having a weak waste management system. In designing your aquaponics unit, using a mechanical filter and biofilter are vital to avoid the accumulation of solids in your fish tank. 

Aside from this, you should also routinely check your system if there are dead fish because it releases proteins and oils that eventually evaporate and create a pungent smell. Another thing to check is the unoxygenated parts of your system. Make sure that they are maintained regularly and adequately. 

The Campbells love finding sustainable and fun ways to increase their independence from traditional brick and motor supermarkets. Aquaponics provides a full lifecycle food source for families and a great hobby. #aquaponicslifestyle

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