Fish Health and Diseases in Aquaponics - Go Green Aquaponics

Fish Health and Diseases in Aquaponics

Fish play a significant role in an aquaponics system. They produce the waste that the plants need to grow and survive. So if you want your aquaponics system to be successful for many years to come, preventing fish diseases should always be your primary concern, since fish are the critical component of your aquaponics system. It is essential you should be able to provide fish with the things they need and ensure their health is always taken care of. In this article, you'll learn about fish health and diseases in an aquaponics system and how to prevent them from infecting your fish.

Fish Selection in Aquaponics

The fish species recorded to have excellent growth rates in aquaponics systems are tilapia, carp (common carp, silver carp, and grass carp), barramundi. Jade perch, catfish, trout, salmon, Murray cod, koi, goldfish and largemouth bass. 

In adding fish to the system, it is essential to acclimatize the fish first, to remove the stressful factors that can cause death to the new fish. The two simple ways of acclimating your fish are:

  1. Keep the new fish in a small aerated container with their original water and slowly add water from the fish tank over a day. 
  2. Slowly allowing the temperature to equilibrate by floating the sealed transportation bags containing the fish in the fish tank for at least 15 minutes. Then slowly add a small amount of fish tank water to the transportation bag. 
Koi in Aquaponics

Fish Health in Aquaponics

Fish behavior is the key indicator of their well-being, so an aquaponics grower must know how to recognize a healthy fish's behavior and understand the signs of stressed or sick fish. The best time to observe fish behavior is during their feeding time. 

Healthy fish behavior during feeding time:

  • Extended fins and straight tails.
  • No lethargy, meaning fish swim in their normal graceful patterns (except for catfish that often sleep at the bottom).
  • Strong appetite.
  • No marks, discolored blotches, streaks, or lines in the body.
  • No rubbing at the sides of the tank.
  • Clear, sharp eyes.
  • No breathing of air from the surface.

Fish Disease in Aquaponics

Fish diseases result from an imbalance system. So an aquaponics grower must have proper fish management practices to have a healthy defense system and ensure fish health. 

Factors that can affect fish health:

  • Poor water quality.
  • Fish stress.
  • Climatic conditions
  • Contaminants and pathogens are present in the system.

Recognizing Fish Diseases

Sometimes, fish diseases still occur even if you apply all the prevention techniques. So it is important to monitor regularly your aquaponics system to recognize fish disease symptoms early and take the necessary action.

Signs of Fish Diseases:

  • Ulcers on the body surface, discolored patches, and white or black spots.
  • Ragged fins.
  • Gill and fin necrosis and decay.
  • Twisted spine and abnormal body configuration.
  • Extended abdomen or swollen appearance.
  • Swollen popped out eyes.
  • Poor appetite.
  • Lethargy or changes in swimming patterns.
  • Odd position in the water, such as head or tail down or difficulty in maintaining buoyancy.
  • Gasping for air on the surface.
  • Fish rubbing or scraping against the fish tank.
Rainbow Trout in Aquaponics

Treatment of Fish Diseases in Aquaponics

Here are some things you need to do if you see signs of fish diseases in your aquaponics system:

  1. Check the levels of pH, ammonia, nitrite, nitrate, and temperature of your system and respond according to the results. 
  2. Immediately remove the infected fish to prevent any spread of disease to other fish.
  3. Place the infected fish in a separate tank and inspect carefully to determine the specific cause or disease. 
  4. Dispose or kill the fish if necessary to avoid the spread of the disease. As much as possible, avoid using antibacterial or anti-parasite treatments that can have detrimental effects on the entire system, including the biofilter and plants. If treatment is necessary, it should be done in a separate tank and never added to the system. 

Common Aquaponics Fish Diseases 

1. Bacterial and Parasite Infections

Fish affected with ectoparasites, molds, and bacterial gill contamination can benefit from salt bath treatment. Salt baths are toxic to the pathogen but not fatal to the fish.

How to Use Salt Bath Treatment:
  1. Remove the infected fish from the fish tank and place it into a salt bath. 
  2. The salt bath concentration should be 1 kg of salt per 100 liters of water. 
  3. Place the affected fish in the salty solution for 20-30 minutes and then transfer to an isolation tank containing 1-2 g of salt per liter of water for 5-7 days. 
  4. Do not use the salt bath water when moving the fish back to the fish tank because the salt concentration will have adverse effects on the plants.

2. Nitrite Poisoning

A new aquaponics system is more vulnerable to nitrite poisoning, especially when they are not yet correctly colonized by beneficial bacteria. However, nitrite poisoning is not just limited to new systems; established aquaponics systems can have nitrite poisoning when the nitrites level goes over six ppm.

Nitrites poisoning can be caused by:

  • Overfeeding the fish
  • Overstocking
  • Improper filter maintenance
  • Washing the grow bed because it also washes away bacteria

Treatment of Nitrite Poisoning:

Lower the nitrite level in the fish tank by:

  • Change 25 - 50% of the water in the fish tank with good quality water and keep changing the water until the ammonia and nitrite level is zero.
  • Stop or reduce feeding, and do not add new fish to the fish tank until the ammonia and nitrite levels are within their range.
  • Remove uneaten fish food and clean the fish tank.
  • Ensure that the tank has enough aeration or add an extra aerator to the system.
  • Adding half an ounce of salt for each gallon of water can prevent methemoglobin buildup. It will also minimize nitrite's influence to strip oxygen from the bloodstream. It is suggested that 1lb of salt is an effective dosage for 150 gallons of water. But as salt does not evaporate, be careful to note down when and how much salt you have added to your tank.

3. Fish Stress

Fish stress is the physiological response of the fish when they live in poor conditions. Stress alone will not kill the fish, but if fish are stressed for an extended period, they will develop diseases that might kill them. So it is better to avoid fish stress as much as possible and know the factors that can cause fish stress.

Causes of fish stress:

  • Overstocking
  • Incorrect temperature 
  • High level of ammonia, nitrite, or toxins in the system.
  • The pH level in the system is out of range.
  • Low dissolved oxygen
  • Inappropriate feeding
  • Poor fish handling.
  • Noise or light disturbance
  • Bullying companions in the fish tank.

Symptom of Fish Stress:

  • Poor appetite
  • Unusual swimming behavior.
  • Rubbing or scraping at the side of the tank, piping at the surface.
  • Red blotches and streaks.
  • Physical injuries.
  • Fins are clamped close to their bodies
  • Fast breathing
  • Erratic behavior

Treatment of Fish Stress

Salt is also used to treat fish stress in aquaponics. Fish react to stress by excreting minerals into the water. When this condition persists for a long time, the salt loss can be fatal for the fish. Adding salt to the water will increase their survival rate because increasing the water salinity will reduce salt excretion and stress to the fish. The recommended salinity level to the fish is 0.5-3 ppt. Keep in mind that adding too much salt can hurt some plants in the system.

4. Fish Fungus

Also known as cotton wool disease or fuzzy fish, the fish fungus looks like a cotton-like growth on the skin or fins. Fungal spores are common in poorly maintained tanks, poor water conditions, or damaged fish tissues from wounds.

Treatment of Fish Fungus

The first and essential thing you need to do is a water test to establish if poor water conditions cause fish disease. If there are other problems, such as ammonia and nitrite levels, you need to ensure that ammonia and nitrite levels are within their ideal range. 

Tilapia in Aquaponics

How to Prevent Fish Stress and Diseases

Below is the list of how you can prevent fish stress and diseases in your system.

  • Purchase healthy fish from a reliable and reputable hatchery.
  • Quarantine new fish in an isolation tank for a few days before adding them to your system.
  • Ensure that the water source is of a reliable origin and good quality. 
  • Remove chlorine from the water.
  • Maintain the key good water quality parameters at all times.
  • Avoid sudden changes in pH, ammonia, DO, and temperature in the water.
  • Ensure adequate aeration to keep DO levels hush at all times.
  • Feed the fish a balanced and nutritious fish food.
  • Remove uneaten fish food from the fish tank after feeding.
  • Ensure that the fish tank is shaded from the direct sunlight.
  • Prevent access of birds and other animals that can be the source of pathogens or parasites.
  • Follow standard hygiene procedures by cleaning, washing hands, and sterilizing equipment.
  • Use one fishnet for each fish tank to avoid cross-contamination of diseases.
  • Avoid loud noise and flickering lights near the fish tank.


Most of the causes of fish diseases in aquaponics are not caused by pathogens but are mainly related to the water quality or toxicity in the system. That is why regular monitoring should be implemented in every aquaponics system to ensure that the water quality parameters are at their optimum levels. So take time to observe and monitor the fish in your system to recognize early symptoms and provide the appropriate treatment. 



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