Common Problems with Aquaponics Systems: Diseases and Deficiencies

This post will help you with some common troubleshooting problems, which you might encounter during your aquaponic gardening journey. Please use this post as a guide to solving some common problems.

Plant health: Help, my plants are sick!

Plants in an aquaponic system are less likely to suffer from diseases and deficiencies than plants in a garden. However, they can still present with the symptoms of a sickness. If just one or two plants look unhealthy, they may be diseased. However, if all of your plants look unhealthy, and particularly if this occurs more gradually, it is likely a system problem.


Plants may suffer from deficiencies, normally denoted by poor growth and fruit set, or discoloration of the leaves. Deficiency is often indicative of a pH issue – it is not that the nutrients aren’t there, but that the plants cannot access them. If pH is in an acceptable range, nutrient deficiencies should be treated as outlined below. Deficiencies are more common in newly established systems. Some of the most common deficiencies are:

Nitrogen deficiency

Yellowing of leaves, beginning at the edges. Increase system input to solve this problem.

Nitrogen deficiency

Potassium deficiency

Poor flowering and fruit set; yellow veins. Supplement with potassium hydroxide for basic systems or potassium carbonate for acidic systems.

Calcium deficiency

Poor fruit set; blossom end rot; burnt tips; leaf curl. Add calcium carbonate; add a quart (liter) of crushed egg shells, sea shells, limestone or coral to the system.

Iron deficiency

Yellow veins; leaves from yellow to white. Supplement with chelated iron to easily solve this issue.


Although more uncommon in aquaponic units than in standard gardens, plants can suffer from the disease. In the case of symptoms such as fungal growths, mildews or spotting on the leaves inexplicable by deficiencies, remove and destroy all affected plants as soon as possible to prevent further contamination. Avoid planting vegetables for the same family for 6-8 months if at all possible.

Healthy plants, no fruit

Nitrogen creates lush, healthy, green leaves, and is important for plant growth. However, too much nitrogen can cause plants to produce lots of healthy foliage at the expense of flowers and fruit. If you have ruled out a potassium or calcium deficiency and have healthy looking plants, but no fruit, you may have an excess of nitrogen in the system. Dilute the system water, reduce inputs, grow leafy greens instead of fruiting plants or add more plants to the system.

If you are growing in an area where bees are uncommon, failure to fruit could also be the result of a lack of pollination. In this case, you will need to hand-pollinate your plants to achieve fruit set.

Cleaning: Help, my growing environment is dirty!

It is important to maintain hygiene and cleanliness in aquaponic systems. A lot of sediment in the fish tank or filters may mean that you are feeding too much. If fish are consuming all food and water is still brown or cloudy, it may be necessary to install a mechanical filter or clarifier. Growing media may also be contributing to the problem if it was not well-washed before use.

Algae is an additional problem which can lead to dirty water. It grows best in anaerobic and sunny conditions. Remember to cover or shade exposed water and to use opaque containers. Ensure that water is sufficiently oxygenated and remove all algae where possible.

Fish: Help, my fish are unhappy!

Fish health is largely indicative of environmental conditions. Fish from a reputable source are unlikely to display ill-health if the environmental conditions of the system are consistent and within the recommended range. However, as the disease spreads quickly, it is important to be aware of common symptoms and act quickly if the illness is identified.

Signs and symptoms of the disease

In addition to water testing, fish behavior and appearance should be monitored daily as an indication of overall health. Behavioral indicators of disease may include:

  • Increased aggression
  • Listlessness
  • Floating at the bottom or top of the tank, unless this is normal behavior for the species
  • Loss of appetite
  • Rubbing or scraping the sides of the tank

Physical indicators include:

  • Difficulty swimming
  • Ulcers, lesions or discoloration on the skin
  • Ragged fins or gills
  • Decaying or moldy gills
  • Swellings or growths
  • Crippling

Dealing with disease

Fish that exhibit any signs or symptoms of the disease should be removed from the system as quickly as possible, as should any with injuries, in order to prevent infection from spreading. Diseased fish can be treated with a salt bath. They should never be consumed.

Salt baths will kill pathogens, without harming fish. A high-concentration salt-bath can be used for 30 minutes, or fish can be placed immediately into a low-concentration salt holding tank. The procedures for moving fish should be followed, with the exception of the change from fresh to saltwater. If no improvement is shown in 7-10 days, fish should be destroyed. If fish do show improved health, a gradual reintroduction to the unit is possible.

Prevention is the best cure for the fish disease. Ensure only healthy fish are added to the system, and that water, fish, and food-sources are parasite and pathogen-free. Good hygiene is also important – never move water between tanks, and wash or sterilize tools and materials between tanks or systems. Wash hands with soap and water before handling system materials.

System measurements: Help, my system is unbalanced!

Sometimes aquaponic systems can become unbalanced with no obvious explanation available. If you find that ammonia or pH levels are of concern and you cannot identify a cause, consider the following points:

  1. Nitric acid is produced naturally in the conversion of ammonia to nitrate. Therefore, more mature systems will eventually become slightly acidic unless water has high carbonate levels, explaining the gradual lowering of pH.
  2. As fish grow, they will produce more ammonia (and require more food). As such, biofilters should be sized for the maximum stocking density, not the initial fish stock.
  3. Low temperatures inhibit bacteria function, and can, therefore, cause ammonia and nitrite toxicity as bacteria struggle to process fish waste that would be easily dealt with at higher temperatures.