How to Identify and Fix Odor in Aquaponics Systems

Aquaponics is a sustainable gardening method in which a grower can grow fish and plants together in one recirculating system. However, whenever fish are mentioned in aquaponics, an unpleasant fishy smell always comes to people's minds. People who are interested in aquaponics ask, do aquaponics systems smell? In this article, we will discuss the odor in aquaponics systems and how to identify and fix it. 

Do Aquaponics Systems Have an Odor?

A properly designed and maintained aquaponics system should have no offensive smell. There might be a slight odor that comes with growing fish, but it will be a slightly earthy or woodsy smell. If your system has an effective waste management system, you should not expect your system to be very smelly.

Anaerobic zones (spaces lacking in oxygen) within the grow beds, pipes, and other areas of your system will result in a foul or sulfur smell. So it is necessary to unclog any anaerobic zones and ensure proper aeration to the entire system to keep it healthy and odorless. When these anaerobic zones are neglected, these minor causes may create a system imbalance that will affect the condition of your fish and plants. 

Aquaponics System

What to Do if Your Aquaponics System Has Odor

If your aquaponics system has a foul odor, you need to identify the odor source to fix it. The three most common causes of unpleasant odor in aquaponics systems are:

  1. Poor waste management
  2. Many anaerobic zones in the system
  3. Dying or dead fish in the system

These situations might not be ideal, but they can be resolved easily. 

1. Poor Waste Management

To prevent waste issues, use high-quality fish food, avoid overfeeding and overpopulating your fish tank. It is also necessary to filter and manage your fish to control waste flow and prevent an imbalance system that might cause a foul odor or kill the fish. 

There are two types of waste found in aquaponics systems: solid waste and dissolved waste. 

  • Solid Waste

The solid waste consists of uneaten fish pellets and fecal droppings. Too much solid waste will cause a foul smell to your fish tank, and it might also kill fish by clogging their gills. Solid waste can also clog the water flow of your system and starve plants of the nutrients it needs to grow. 

How to Remove Solid Waste in Aquaponics Systems 

Reducing solid waste is the first step in preventing odor issues in your system. Mechanical filtration or clarifiers is the most common method of reducing solid waste in your system. The four main types of filtration systems used in aquaponics are:

  1. Swirl filter: A swirl filter is a large barrel with an inner basket. The basket filters the solid waste out. Solid wastes collect at the bottom of the barrel because of the slow water flow. This filter needs to be cleaned and maintained regularly.
  2. Raft water filter:This is a dual-chamber filter. Large particles are removed in the first chamber, while the fine particles are captured in the second chamber. This filter required an air stone to oxygenate the water. 
  3. Radial flow filter: The radial flow filter uses a large barrel with water from the fish tank piped into the middle of the barrel. The solid waste falls into the bottom of the tank while the clear water is piped out from the top.
  4. Drum filter: The drum filter is a large filter with a rotating mesh drum in the center. The fish water is pumped into the outer chamber, and a pump pulls the water from inside the mesh drum. The water is filtered when it is pumped out of the mesh. 
  • Dissolved Waste

Dissolved wastes are solid wastes that have broken down into small particles. These wastes can cause oversaturation of nitrogen, ammonia, and phosphorus, which can cause turbidity, toxicity, and temperature changes in your system. Although nitrogen, ammonia, and phosphorus are highly harmful, they are also essential nutrients, so they should be carefully monitored. To prevent dissolved waste problems in your aquaponics systems, you need to install a biofilter

How to Remove Dissolved Waste in Aquaponics Systems

Most aquaponics systems have enough beneficial bacteria that break down dissolved waste into nutrients for the plants to use. Dissolved waste is rarely a problem in aquaponics. However, if you use the Nutrient Film Technique (NFT) method, you need a biofilter to manage dissolved wastes. A biofilter is a container that holds porous materials and provides a surface area for the bacteria to live. An air pump is also required to addoxygen to the biofilter to help the beneficial bacteria thrive.

2. Many Anaerobic Zones in The System

Unmanaged anaerobic zones or parts of your system that lack oxygen are another reason why some aquaponics systems have odor problems. These anaerobic zones are dangerous to fish and plants and can cause a bad sulfur smell. Regular cleaning and maintenance check of your system's pipes that might be clogged or unoxygenated areas is necessary to prevent anaerobic zones. You can also add air stones to these zones to lessen the sulfur smell and remove anaerobic zones from your system. 

A Dead Fish in Aquaponics

3. Dying or Dead Fish in The System

A dead fish is one of the most common causes of a foul odor in aquaponics systems. Dead fish smell horrible and release toxins into your system. So if you find a dead fish, you need to remove it to prevent further smells and toxins from being released into your system. 

It is also necessary to know why a fish died in your system. A dead fish indicates a problem in your system that should be addressed. Here are some common causes of dead fish in an aquaponics system. 

  • Not enough oxygen
  • Poor water quality
  • Overfeeding or underfeeding

If you see a dead fish in your system, here are a few steps to follow:

  1. Remove the dead fish immediately.
  2. Check the color and the quality of the water. If it is brown and sludgy, clean your filtration system and pipes or add air stones or a filtration system.
  3. Check the pH and ammonia levels and adjust them if they are too high or low. Ensure that they are at the ideal level at all times.
  4. Check if your fish gets enough oxygen. Add air stones or air pumps to help oxygenate the water in your system.
  5. Remove sick fish in your fish tank. 


One of the main reasons an aquaponics system produces unpleasant smells is poor management practice. A properly designed and maintained aquaponics system should have little to no smell. If there is an odor, it should be earthy and natural. Any foul-smelling odor indicates an imbalance system that you should immediately investigate. Identifying and fixing the foul odor problem of your aquaponics system can be easy if you know where to look. Thank you for reading our article. If you're new to aquaponics and want to learn more, read our article "The Ultimate Aquaponics Beginner's Guide."


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