9 Reasons Why Your Aquaponic Fish Are Dying

Aquaponics is a modern farming practice that combines fish-rearing and specific crop-type farming in a self-sustaining controlled environment. However, sometimes things don’t go as planned, and your fish may die due to an imbalance in the ecosystem.

Here are 9 reasons why your aquaponic fish are dying:

  1. The water in your system is not moving.
  2. Your water filter is failing.
  3. You aren’t monitoring the system properly.
  4. Your fish have a disease.
  5. Your water’s quality is poor.
  6. Improper ammonia, nitrate, & pH levels in the water.
  7. Fish-bacterial-plant population imbalance.
  8. There’s too much carbon dioxide in the water.
  9. Improper fish nutrition and imbalance in micronutrients.

As you can see, there are quite a few things that can kill off your fish population. In this article, I’ll describe these common issues in-depth and give you some advice on how to recover your tank after the death of your fish. I’ll also teach you how to prevent fish death in the first place. 

1. The Water in Your System Is Not Moving

When working with an aquaponic system, being vigilant and aware of what’s going on in your fish enclosure is critical. That’s because, sometimes, the tank’s systems fail, making the conditions inside unsuitable for sustaining life.

However, you can’t always catch an issue when it arises, which may mean some lost fish.

If the water in the fish tank accidentally drains out, the fish will die. Likewise, if water movements in the aquaponic system stop, it could be fatal for the fish population.

That’s because such blockages reduce oxygen levels in the water. If there isn’t enough oxygen, your system may become deadly to aquatic creatures.

Water circulation problems can result in stagnating toxic fish wastes such as ammonia. Such high concentrations of these wastes are harmful to fish survival, and the fish will start to die if you stop pumping out the fish’s excrement.

When your water is stagnating, you’ll need to add extra air pumps or siphons to increase the oxygen concentration in the water.

The best way to ensure your water gets plenty of air circulation is to install venturi siphons. These pumps are beneficial for deep-water culture systems that support large-scale commercial farming.

The venturi siphon pulls in the outside air as water flows through them. These tapered pipes can redirect your water, causing faster water flow. In this way, venturi siphons are like man-made whirlpools that draw in fresh air from the outside environment.

This aspect helps air circulate through the water, raising the water’s dissolved oxygen levels.

Deploying submersible impeller pump units into your enclosure is also a viable option, especially in large-scale aquaponic farms. These pumps have a good pumping capacity and will act as the water circulatory system of the aquaponic system as a whole. Reducing the number of piping connections from the pumps to the fish tank is essential because the flow rate declines with every new link.

The installation of airlifts could help with the water stagnation issues in aquaponic units. This technique is ideal for small-scale aquaponic farms.

Airlifts pump air to the tank’s bottom, triggering water movement as they shoot bubbles up to the surface. Airlifts are suitable for deep tanks and aren’t susceptible to clogs like the submersible impeller pumps.

Also, it’s essential to constantly monitor the flow rate to understand the amount of air in the system. An aquaponic system with a flow rate of about 4-8 liters (1-2 gal) per minute suffices optimal dissolved oxygen in the water.

2. Your Water Filter Is Failing

Your filters usually remove leftover food, excrement, debris, and algae from your tank, helping you keep the good stuff in while taking the bad stuff out.

However, when the filter malfunctions, this organic waste leftover will accumulate, causing the water to become toxic to your fish. Additionally, improper functioning of the biofilters results in the accumulation of ammonia and fish excrement in the water.

High levels of ammonia-based fish wastes in the water create a toxic environment for fish. When this happens, the fish start dying, one by one. Bacterial colonies can’t thrive when a biofilter malfunctions. So, the whole system will begin to go out of whack when a filter fails.

You simply must clean the filter when it gets clogged. Adding larger, more powerful filters can help reduce the number of times you have to change the filter, but it’s best just to change the filter every few weeks or as recommended by your filter manufacturer.

Be sure to purchase replacement filters that fit your filter model with no gaps or leaks. These gaps could introduce more clogs and algal growth, forcing you to replace the filter frequently.

3. You Aren’t Monitoring the System Properly

Some of the most catastrophic aquaculture failures happen due to human mishandling. Aquaponics technologies require some level of expertise to install, run, and maintain for optimal results.

However, sometimes the people running the day-to-day operations on these farms have inadequate know-how to run the aquaponic farm facility. This knowledge gap leads to mistakes, which may result in fish deaths.

One common error is insufficient monitoring of aquaponic systems. For example, if a technician doesn’t know the ideal water pH for their fish, they may not recognize a problem when they see it.

Likewise, clogged filters and improper cleaning of fish enclosures can result in fish deaths due to anoxia (lack of oxygen).

Exposing the fish enclosure to too much sunlight can be catastrophic. UV exposure can affect the photo-sensitive bacterial colonies in your water, and if they grow too much, they may reduce the tank’s airflow and trap fish waste.

This overgrowth leads to the accumulation of aquaculture effluents in the water that causes fish death.

Many human errors can affect your aquaponic fish’s health, so training yourself and the people who work with you is crucial. Do as much research as you can before setting up your aquaponics system, and don’t be afraid to ask questions.

Developing a daily routine or a checklist for your system maintenance can ensure that you and everyone else who helps you manage your system are all on the same page. Be sure to monitor filtration, oxygenation, pH, temperatures, and plant health every day to prevent death in your fish.

4. Your Fish Have a Disease

Fish diseases account for a significant proportion of fish fatalities in aquaponic systems. Some of the most common causes of fish diseases and death include fungal, viral, or bacterial infections. These diseases are predominantly categorized into two, namely, infectious and non-infectious fish diseases.

Fish disease control is one of the significant challenges caused by the collapse of aquaponic systems.

One of the key attractions to aquaponics farming is that it is self-sustaining and requires minimal chemical interventions, making the system mimic a natural ecosystem.

The sustainability aspect of aquaponics is associated with system design, fish nutrition, fish health, and pathogen control. However, this is also a shortcoming because it creates a conflict of interest when infectious and non-infectious diseases wreak havoc on your tank.

Due to the complexity of the aquaculture and plant culture aspects of the aquaponic system, the remedies to disease aren’t that easy to use.

That’s because when you add medicine to the tank to cure your fish, it will sit in the water, where it will later move to your aquaponic plants. These medicines can make edible aquaponic plants toxic, so it’s crucial to investigate your treatment options thoroughly before adding any chemicals to the tank.

Such complexities of the aquaponics systems create uncertainties and dilemmas that can be challenging to negotiate with.

Fish can be carriers of pathogens, which under specific optimal aquatic environments, quickly evolve into fully-fledged bacterial diseases spreading to other fish. Non-infectious conditions are primarily from external environmental factors including, unbalanced diets, poor nutrition, or genetic defects of the fish.

The primary strategy to reduce fish fatalities should include early detection and mitigation or complete avoidance of fish diseases by taking proactive preventative steps. Ensuring that vulnerable fish don’t contact potential disease pathogens can help reduce fish deaths.

 Here are some tips to help you eliminate and prevent disease in your hydroponic system:

  • You should select fish species with high resistance to the most common fish pathogens in aquaponic systems.
  • Minimize factors that could introduce stressors.
  • You should avoid high fish stocking densities since overcrowding increases infection vulnerability in disease outbreaks.
  • Remove excess food from the fish tank 5 minutes after every feeding.
  • In case of any fish deaths, they should be promptly removed from the tank, providing proper sanitation.
  • Always ensure the fish feed contains immuno-nutrients that strengthen fish immunity, reducing infection rates in the event of disease exposure.
  • When fish get older, they become less vulnerable to diseases. Therefore, you should always segregate fish according to age.
  • Feed your fish a nutritious and balanced diet.
  • Isolate new fish in a non-aquaponic tank before adding them to the system.

Also, if you notice disease in one or more of your fish, remove them from the aquaponic system immediately. That way, you have a better chance of containing the condition before it spreads to your other fish. Then, clean the enclosure and refill it with clean, dechlorinated water.

5. Your Water’s Quality Is Poor

Fish need water to survive—we all know that. However, fish don’t just need water. They need certain types of water enriched with oxygen, a gentle pH, and plenty of helpful bacteria and plants that keep the tank sustainable.

Through water, fish can uptake dissolved oxygen, obtain support against gravity, and remove toxic metabolic wastes.

Several parameters indicate changes in water quality and condition in an aquaculture setting. These include dissolved oxygen levels, nitrites concentration, water pH, and ammonia—all of which should be within certain allowable limits.

Typically, fish can resist disease-causing pathogens through physiological changes to maintain homeostasis as long as the water conditions are stable. This ability to restore stability through physiological change is called an allostatic load.

When the allostatic load is minor, your fish’s resistance to disease is high. However, issues with water quality tend to raise the allostatic load. When this happens, the poor water quality will stress the fish and make them more vulnerable to diseases and parasites.

Some elaborate indications of water changes are fish growth rate, size, stocking density, and fish feeding rates. These physiological and behavioral displays could suggest that the water quality is changing and that you need to immediately do something about your enclosure’s water.

When you add poor-quality water, such as tap water, to your aquaponic system, your fish will notice the difference immediately.

Tap water is primarily considered unhealthy for fish due to the high chlorine contents. Such an abrupt change in water conditions can also stress your fish out. With the two factors combined, some of your fish may die quickly.

Monitoring your system’s water is probably the most critical part of maintaining a healthy aquaponic garden.

To catch issues early, you need to check for pH, oxygenation, and filtration every day. Only use fish-safe water for your system, whether that means purchasing single gallons of distilled water, purchasing rain barrels, or conditioning your water before you put it in the tank.

6. Improper Ammonia, Nitrite, and pH Levels in the Water

When ammonia levels in the water are high, the pH of the water is vastly affected (becomes lowered).

High concentrations of ammonia may end up being reabsorbed through a fish’s gills. Ammonia toxicity leads to neurological disorders in fish, as it affects the central nervous system. Ammonia toxicity results in stunted fish growth and increases fish mortality rates.

High ammonia levels in water are also stressful for fish. Your aquatic creatures will respond by releasing stress-related hormones-corticosteroids, adversely impacting fish welfare.

Most fish species are non-tolerant to nitrite in water. The nitrites are taken up through the gills via active transport.

When your fish breathes in these chemicals, they oxidize their blood, resulting in fatal hyperventilation.

Therefore, conducting regular checks on water quality, guided by measuring the above parameters to make sure they’re within acceptable limits, is crucial for fish welfare.

7. Fish-Bacterial-Plant Population Imbalance

It’s crucial for there to be a balance between fish population, bacterial colonies, and plant population.

That’s because, in an aquaponic system, these three players co-exist, depending on each other for survival. Therefore, the whole tank’s quality of life will decrease when you don’t have enough bacteria to break down your fish’s excrement.

Likewise, when the rate of nitrification is low, the plants won’t receive essential nutrients for proper growth.

In turn, there’ll be little dissolved oxygen available in the water for fish respiration. This depletion in aeration leads to mass fish fatalities, and in large aquaponic farms, this means stoppage of operations and incurring substantial economic losses.

Expertise is necessary to ensure an appropriate balance in the quantity of fish, bacteria, and plants. If you keep everything balanced, only then can you guarantee the self-sustainability of the system and minimize fatalities.

This interdependence points to the importance of a well-balanced fish, bacterial colonies, and plant population for proper sustenance.

Otherwise, imbalances of these factors lead to the death of the fish population in most aquaponic farms.

8. There’s Too Much Carbon Dioxide in the Water

The predominant source of carbon dioxide in aquaponic systems is the fish themselves. High carbon dioxide content in water isn’t conducive to fish survival and could significantly affect fish welfare.

When the carbon dioxide levels in water are high, the fish can’t release it into the water. This over-absorption results in the accumulation of carbon dioxide in your fish’s blood, a condition known as hypercarbia.

When this happens, the fish’s blood pH lowers, causing carbon dioxide toxicity. During hypercarbia, the fishes’ physiological responses include gaping their mouths and their gill laminae turning bright red.

9. Improper Fish Nutrition and Imbalance in Micronutrients

Fish diet is the primary determinant of the capacity of any aquaponic system. Most fish feeds are generic, only considering the appropriate mix of nitrogen and energy, ingredients, and particle size of these feeds.

However, all fish need different things to survive, so you’ll have to do your research to give your specific fish species what they need.

Micronutrients such as iron, potassium, magnesium, and zinc are essential for fish to stay happy and healthy. Iron is vital for the transportation of oxygen in the fish blood via red blood cells.

However, too many or too few micronutrients mixed in fish diets could be detrimental to fish health.

For instance, excess manganese in fish diets could significantly reduce intestinal immunity. On the other hand, zinc may be essential in fish bone formation and keeps a fish’s metabolism running swiftly. Meanwhile, excessive quantities of zinc in the feed will inhibit calcium absorption, which is crucial for bone strength.

A fish diet lacking zinc fortifications makes the fish susceptible to dwarfism and weak immunity, exposing the fish to disease contraction and high mortality. Also, high phosphorus content in the water may cause the rapid growth of algae in the aquaponic system.

Overfeeding can cause chemical imbalances in the tank or introduce system errors. Large uneaten food particles may be difficult to maneuver through the piping system, causing pipe clogs that cause water stagnation and alter water quality.

So, as you can see, balance is critical, and too much or too little of one thing can cause death in your fish or increase bacterial imbalances in the tank.

Therefore, it’s essential to provide your fish with the proper nutrients, guaranteeing better fish health and reducing vulnerability and fish fatalities.

Precautionary Steps in Running Aquaponics

Use Dechlorinated, Conditioned Water

Water is the primary medium through which nutrients reach the plants and form the dwelling places for fish. 

Since your water could make or break your system entirely, you should always select appropriate water sources for aquaponics.

Rainwater, distilled water, and filtered water are suitable for filling up your fish enclosures. Just be sure to avoid mineral and spring water since they contain a lot of minerals that could imbalance the water in your tank. 

Municipal water contains chlorine, fluoride, and many minerals, which need extraction before use. Using water softeners can also be risky because such products contain sodium. You can use carbon filters or other filtration methods to remove impurities from tap water that can harm your aquaponic fish.

Test Your System Frequently for Performance

In the day-to-day handling and running of the aquaponic system, conducting various parameter checks and tests to ensure a properly working system is vital. The aquaponics design promises self-sustenance after installation, but only with good maintenance. 

A skilled aquaponics manager needs to conduct these checks. Usually, it’s best to check these parameters every day or every other day to prevent any sudden fish deaths. 

Some important parameters to check include: 

  • Water pH level
  • Water temperature
  • Ammonia levels (Total Ammonium Nitrogen – TAN)
  • Water hardness level
  • Vital nutrient checks (both macro and micronutrients)
  • Dissolved oxygen levels

Checking these parameters can ensure that your tank is balanced, thus ensuring that you don’t wake up to any floating fish bodies. These tests can help significantly increase production on a commercial-scale installation. 

Checking these things frequently can reduce the chance of water quality fluctuations, which cause fish stress and detrimental allostatic load responses. 

Below are recommended water quality checks in aquaponics systems to avoid fish deaths. (This may differ depending on the type of fish you have.)

ParametersIdeal Test Results
Water pHpH 6 – 7
Water Temperature65–85°F
Total Ammonium Nitrogen<1 ppm
Nitrates level<1 ppm
Nitrite levels5 –150 ppm
Dissolved OxygenØ  5ppm

Final Thoughts

Excellent fish health is the main determining factor in an aquaponic system’s success. Therefore, it’s imperative to check and take proactive steps to ensure good fish health and welfare to prevent fish fatalities.

Negligence is the primary cause of fish death in aquaponics systems. Any neglect of duty or mistaken malpractice could be catastrophic to the fish population.

People running an aquaponics farm should seek necessary training on running, caring for, and troubleshooting problems when they arise. Such education would help these farm managers to conduct early detection and prevention of fish deaths.

Alexander Picot

Alexander Picot is the founder of TheGrowingLeaf.com and its lead content writer. He created the website in 2022 as a resource for horticulture lovers and beginners alike, compiling all the gardening tips he discovered over the years. Alex has a passion for caring for plants, turning backyards into feel-good places, and sharing his knowledge with the rest of the world.

Recent Posts