How to Prevent Fish Diseases in Aquaponics - Go Green Aquaponics

How to Prevent Fish Diseases in Aquaponics

If you are an aquaponics grower, you understand that keeping the fish healthy is very important. Fish disease is common in aquaponics systems, especially if they are not well monitored and well-maintained. The fish disease can lead to serious problems that can affect the plants, fish, and the entire system. 

If you want your aquaponics system to succeed, then keeping your fish healthy is a priority. This article will discuss some aquaponics most common fish diseases and how to prevent them.

Understanding Fish Diseases in Aquaponics Systems

Fish disease usually occurs when you fail to maintain your aquaponics system properly. Pathogens such as bacteria, parasites, and fungus can propagate rapidly and enter the system by introducing fish or expanding organisms in the fish tank.

Abnormality or unbalance between your system’s environment, pathogen agents, and the fish in your fish tank will probably lead to various problems. This is why maintaining good water quality through regular management practice is essential. With regular maintenance practice, not only will you be able to prevent various diseases, but it will also ensure the entire system is well-maintained and running smoothly. 


Fish in Aquaponics

Cause of Fish Disease

Fish disease in aquaponics is always the result of abiotic and biotic factors. Abiotic are non-living chemical factors that affect toxicity or water quality. Biotic factors are living pathogens or organisms that can directly or indirectly affect their environment. Like other animals, fish also carry bacteria, viruses, fungus, and parasites. Though not all these bacteria are harmful, some of these microorganisms can potentially cause fish diseases. 

 The following factors can cause fish disease in your aquaponics system.

  • Adding new fish to the system

  • Environment or poor water quality

  • Fish stress

  • A poor or unbalanced diet

  • The equipment used in the system is not suitable for the fish

  • Not getting along with other fish species in the fish tank

Common Fish Disease in Aquaponics Systems

To help you identify and accordingly act on your fish health issues, here is the list of causes and symptoms of common fish diseases of aquaponics fish. For a more list of fish disease in aquaponics, click here. 

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. The causes of nitrite poisoning are new tank syndrome, failure of the biofilter, fish overcrowding in the fish tank, recently washed biofilter or media, reduced water flow, and temperature drop.


  • breathing difficulty

  • darker gills

  • brownish blood

  • abnormal swimming

  • gathering near the water's surface

  • Lethargy

  • redness around the eyes and fins.


  • immediate (20-50%) water replacement

  • add biofilter media

  • reduce fish density

  • stop feeding

  • add chloride

  • improve aeration

  • adjust the temperature

  • avoid fish disturbance

Temperature Stress

Temperature stress is caused by the rapid change in temperature or when the temperature is not in its normal range, bad insulation, or faulty system management. The most common cause of temperature stress is lack of heating or insulation and improper management of the system. 


  • lethargy

  •  mold disease (hypothermia)

  • dyspnea (hyperthermia)


  • insulate the fish tank

  • add a water heater

  • shade the tank

  • ventilate at night

  • use a cooling system

  • use a greenhouse in cold seasons

Ammonia Poisoning

Excessive ammonia is harmful to the fish. Increased pH levels may cause ammonia poisoning in the fish tank. The causes of ammonia poisoning are new tank syndrome, biofilter failure, too many fish in the tank, overfeeding and failure to remove uneaten fish food, reduced water flow, decreased oxygen, and temperature drop, which inhibits the nitrifying bacteria.


  • abnormal swimming patterns

  • not eating during feeding

  • darker gills

  • larger gills (hyperplasia for chronic toxicity)

  • redness around the eyes and fins.


  • immediate (20-50%) water exchange 

  • reduce pH with acid buffer

  • add biofilter media 

  • improve oxygenation

  • adjust temperatures

  • stop feeding

Fin Rot

Fin rot is often caused by bacterial infection from different agents, poor water conditions, and bullying from other fish. 


  • damaged fin ray exposed

  • loss of color

  • Bleeding

  • ulceration


  • identify the causes

  • treat the infected fish in a separate tank and provide medicated fish food with antibiotics (chloramphenicol or tetracycline) or dissolve the antibiotic directly in the water

  • keep sick fish separate until fully recovered

White Cotton Saprolegnia

White cotton Saprolegnia is typically a fungus disease caused by temperature drop, concurrent causes of acute stress, and transport stress. 


  • white, brown, or red, cotton-ish growth on the fish surface

  • ocular lesions as cloudy eyes causing blindness and loss of the organ


  • prolonged formalin or salt bath

  • treatment of eggs with hydrogen peroxide, or prolonged immersion in methylene blue

  • lesions may be treated with a cloth soaked with povidone-iodine


Aquaponics Fish Diseases

Preventing Fish Diseases in Aquaponics

As mentioned before, healthy management practice is the key to keeping your fish healthy and happy. Below is a list of how to maintain healthy fish in your aquaponics system.


Since many issues are related to the food, ensure to feed your fish only with nutritious and healthy food. Stick to the recommended fish feed for the respective species and always choose quality over quantity. Depending on the fish species you raise, you can also give alternative fish feed to your fish. Tips for feeding your aquaponics fish. 

  • Always feed fish with balanced and nutritious fish feed.

  • Remove uneaten fish food from the fish tank after feeding to check for unusual behavior.

  • Always observe fish behavior during feeding

  • Keep your fish food in a dry, cool place. If your fish food is kept in the wrong conditions, it might develop mold that may cause fish diseases. 


No matter what fish species you choose to raise, make sure to educate yourself on their growing requirements. Although most aquaponics fish are hardy and can survive in different water conditions, providing the ideal environment for them is key to a successful aquaponics garden. 

Fish behavior is the key indicator of their well-being. An aquaponics grower must know how to recognize a healthy fish's behavior and understand the signs of stressed or sick fish. 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 allow 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. 

Below is The List of How You Can Prevent Fish Disease 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.

  • Ensure that the fish tank is shaded from the direct sunlight.

  • Prevent birds and other animals from entering your system 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.


Fish health is very important in aquaponics systems. A healthy fish is necessary for the overall success of your aquaponics system. So when you decide on the fish species for your system, know its growing requirements and provide the ideal environment for them. This way, you can be sure you are preventing fish disease and enjoying a bountiful harvest from your aquaponics system.

Always keep in mind to always remove the infected fish from the fish before treating it with a salt bath or other fish treatment methods. Thank you for reading our article. Subscribe to our newsletter to get regular aquaponics updates. 



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