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Fish Disease and Treatment

Fish culture is inherently a messy business. Bacterial pathogens and parasites that affect fish are naturally occurring and opportunistic by nature. Good management, proper husbandry practices, and daily observation of fish can prevent many issues associated with fish health. Proper management techniques in the fish production of the aquaponics system should include: system design, water quality monitoring and correction, equipment maintenance, feed storage, fish observation to remove sick or dead fish, and worker sanitation. Common external physical signs of fish disease include:

  • Hemorrhage: an abnormal discharge of blood

  • Lesions: a defined area of diseased tissue such as an ulcer, blister, or canker

  • White spots or pustules

  • Pale or swollen gills: often seen with fish "gulping" at the surface of the water for air

  • Dark coloration

  • Excess mucus on the skin or gills

  • Sloughing of skin

  • Emaciation

  • Distended abdomen

  • Exophthalmia: pop-eye

There are four major groups of pathogens related to fish culture: fungi, bacteria, viruses, and parasites. Common fish diseases and their treatment are listed below. Typically, diseases seen in aquaponic production systems are a result of environmental or physical stress (Figure 20). Stress can stem from 1) rough or excessive handling, 2) confinement of non-domesticated species of fish into tank systems or inappropriate stocking densities, 3) improper feed supply, feeding regiment, or nutrition and 4) poor or unsuitable water quality conditions.


In preparation for stocking fish, biofilters must be broken in (populated with established bacteria before fish are stocked in the system) and water quality parameters must be within acceptable ranges for the species of fish being cultured. Once fish are on-site, and before they are stocked into new or existing production, they should be quarantined and treated prophylactically for external parasites using salt, formalin, potassium permanganate, or other approved treatments. Treatment must happen outside of the production system, as chemicals introduced in the aquaponic system will cause the biofilter to crash and the whole process will have to be started over. Fish should also be observed for any physical abnormalities in appearance or behavior. Many diseases are first detected by observing abnormal swimming patterns.

Signs of abnormal behavior include whirling, flashing, bobbing, gasping, or side-swimming. Quarantine facilities and general good fish-handling protocols should include 1) washing hands before and after interaction with tanks, equipment, feed, or fish, 2) using nets and other equipment only in the quarantine or production area, 3) thoroughly drying or even bleaching between uses (via bleach buckets or spray bottles) to kill bacteria, fungus, and parasites, and 4) working in quarantine areas as the last task of the day to prevent cross-contamination. Arthur et al. (2008) provide a comprehensive overview of quarantine procedures for live aquatic animals.

Once fish have been stocked and the system is in operation, it is critical that water chemistry be conducted regularly and that resultant numbers are checked as acceptable for both fish and plants. Any necessary adjustments should be made as soon as issues are identified, as water chemistry problems will not self- correct. Early detection and intervention is the best measure to make sure that production is maximized for both time-to-market and crop yield.

During production, fish that are crowded into tanks for intensive culture can get stressed, which is manifested several ways. Stressed fish can go off feed (stop eating); hit the sides of tanks, causing abrasions to their body or fins; nip at each other in aggression; and even jump out of tanks, resulting in death.

Stressful culture conditions weaken the fish's immune systems, leaving them more susceptible to bacterial and fungal infections. Typically, at the first sign of illness, fish will stop eating. At this point, medicated feed is useless, and a chemical treatment is required.

Another way fish become diseased through stress is poor water quality conditions. This can be a result of poor water chemistry and inadequate water conditions. For example, fish become stressed during acute or chronically low levels of dissolved oxygen and are more susceptible to disease. Another example is occasional overfeeding of fish. The excess protein breaks down into total ammonia-nitrogen, which breaks down further into toxic components of un-ionized ammonia-nitrogen and nitrite-nitrogen. The biofilter component is not sufficient to convert these compounds to nitrate, leading to stress on the fish from poor water quality. These toxic components are further exacerbated by issues such as high pH and increasing temperatures.

To prevent stress on the fish, a general rule of thumb is to stop or reduce feed input in the system:

  • When temperature is outside of species range

  • When fish are sick or stressed

  • 24-48 hours before/after transport

  • 24 hours before sampling

  • 3-4 days before processing

  • When low DO is present

  • When water quality parameters are sub-par

If fish stocked into production become sick, they should be removed from the system immediately for treatment or disposal. Water amendments should be made promptly, stocking rates should be checked, water flow should be checked, and water exchanges may be necessary. There are no good treatment options for treating systemically in production, as chemicals cannot be used with coupled aquaponic systems. Fish can be removed or isolated, treated in containment, and reintroduced at a later date.

System design plays a role in disease prevention. Tanks used for fish culture should be round and preferably have a conical bottom for removal of settle-able solids. Design should be such that tanks are easy to disinfect, can be isolated individually from the rest of the system, and have windows to view fish in the water column.

Source: Janelle Hager, Leigh Ann Bright, Josh Dusci, James Tidwell. 2021. Kentucky State University. Aquaponics Production Manual: A Practical Handbook for Growers.

Kentucky State University

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