10 Reasons Why Your Aquaponic Plants Are Dying

Aquaponics is one of the latest developments in agriculture where experts combine the key elements from aquaculture and hydroponics for fish and plant farming. The idea sounds clever and logical as you can reap the benefits from both systems at the same time. However, it’s rather challenging to ensure that plants stay alive.

Here are 10 reasons why some of your aquaponic plants are dying:

  1. Some plant species aren’t suitable for aquaponics.
  2. Insufficient water, dissolved oxygen, and carbon dioxide.
  3. There’s a nutrient imbalance.
  4. Your aquaponic plants are infested with pests.
  5. Harmful microbes are growing and thriving.
  6. You’re not managing the water pH properly.
  7. You’re using treatments toxic to plants.
  8. You have a defective or dirty filtration system.
  9. You have an unstable power supply.
  10. You have poor water quality.

Although there may seem to be a lot of things that could go wrong and lead to plant death in aquaponics, in reality, they’re avoidable and manageable. This article will explain the possible reasons in detail so you can recognize the issue in your aquaponics system more efficiently and apply the best remedy.

1. Some Plant Species Aren’t Suitable for Aquaponics

An aquaponics system can accommodate many varieties of plants, such as green, leafy vegetables like spinach, basil, and cabbage. Unfortunately, however, not all plants can grow well in this kind of setup. The lack of an appropriate substrate, space, or physical support in an aquaponics system makes it unsuitable for some plants.

Some of the plants that can’t thrive well in an aquaponics system include:

  • Root crops (potatoes, carrots, onions)
  • Vining crops
  • Plants that require a lot of space
  • Crops with very long root systems
  • Tall plants like shrubs
  • Plants that bear heavy fruit

These plants have specific requirements that need to be met, and failure to do so may lead to a weak, unprofitable yield or even plant death. It’s best to grow them under normal conditions in the soil where they can get enough nutrients and space for their roots to grow.

Vining crops need plenty of space and something to hold onto as they climb, and it isn’t easy to set up in an aquaponics system. On the other hand, plants with pretty heavy fruits can damage the aquaponics setup with their excess weight.

2. Insufficient Water, Dissolved Oxygen, and Carbon Dioxide

Water, oxygen, and carbon dioxide are essential to ensure plant survival and good health in an aquaponics system. All three components must be monitored and maintained to ensure the system’s proper function. 


Sufficient water is one of the critical components required to keep an aquaponics system running. Not having enough of it would be detrimental to both the plants and the fish in the system. Fortunately, not much water is lost through other means because it’s efficiently recycled in the system.

Nonetheless, farmers must regulate the amount of water as some could be lost naturally through evaporation and consumption by the plants. In addition, contaminated water must be removed and replaced with fresh and chemically-tested water.

Dissolved Oxygen

Dissolved oxygen (DO) is another essential component in the system. It’s necessary for the fish and nitrifying bacteria to produce or convert chemical elements and nutrients that plants need to survive and yield abundantly.

You can measure dissolved oxygen daily for a month or two for newly set up aquaponics systems. Ideally, the daily average of DO must be between 5ppm and 8ppm. If it’s established and remarkably maintained, you can check the DO concentration less frequently.

Moreover, it’s important to note that temperature can affect the amount of dissolved oxygen the water can hold. In summer, when the water is warm, it can keep less DO. On the contrary, it can hold more in winter. 

As such, it’s necessary to monitor the water temperature and DO concentration at regular intervals every season so that you may quickly make adjustments when necessary. For instance, you may check it once or twice a week and keep a record for future reference.

Carbon Dioxide

Plants need carbon dioxide to perform chemical reactions, such as photosynthesis and food production. The atmosphere and the fishes in the system serve as the primary source of this compound. If there’s insufficient oxygen for the fish, it may lead to less carbon dioxide for the plants, resulting in poor plant health or even death.

Luckily, carbon dioxide is widely available in the atmosphere. Meanwhile, too much carbon dioxide in the water may also be harmful to the fish and affect the system negatively. It’s, therefore, necessary to maintain the level below 20ppm.

3. There’s a Nutrient Imbalance

In an ideal aquaponics system, plants feed on nutrients produced from fish waste. However, an imbalance between the number of fish and the number of plants and several other factors may lead to nutrient deficiency or unavailability to the plants.

Some of the essential and trace nutrients plants need include:

  • Nitrogen
  • Potassium
  • Phosphorous
  • Calcium
  • Magnesium
  • Sulfur
  • Boron
  • Chloride
  • Copper
  • Iron
  • Manganese
  • Molybdenum
  • Zinc

Most of the nutrients the plants need can be provided by a mature system as long as it works well. However, those that aren’t readily available such as iron, calcium, and potassium, need to be supplemented.

Freshwater or deep-well water may contain trace amounts of some essential minerals that could greatly help the system. Therefore, it’s necessary to have the water source checked by a certified laboratory to check the components and treat some problems when necessary.

It’s important to note that when plants in an aquaponics system show signs of nutrient deficiency, it may not be because the mineral isn’t available in the system. It could be because of water pH, temperature, or humidity that may limit the plants’ ability to absorb the nutrients.

Therefore, you must conduct a water chemical analysis before adding nutrient supplements into the system. Remember that excessive amounts of certain minerals may prove detrimental to the plants and fish and may even promote the growth of unwanted microbes and algae.

4. Your Aquaponic Plants Are Infested With Pests 

Pests are common enemies of plants that can hinder their growth or damage the edible parts. They also prove troublesome in an aquaponics system where the use of chemical pesticides is highly discouraged, as they can negatively affect the other components.

That’s why it’s important to screen new plants in an isolated area to remove any visible signs of pests and ensure the plants’ health before introducing them into the system. This way, you can avoid infecting the other plants already set up in the system.

Here are some aquaponics plant pests that farmers need to be wary of:

  • Aphids
  • Spider mites
  • Whiteflies
  • Thrips

These pests have to be dealt with immediately because they reproduce rather quickly. 

Caretakers have to remove them by hand or other tools manually, but it takes some time to get rid of all of them. However, those who don’t have much time to deal with pests manually can use safe methods to solve the problem.

Here are some natural ways to get rid of pests on aquaponics plants:

Introduce Insects That Feed on Plant Pests

Ladybugs are natural enemies of aphids and spider mites as they can significantly reduce the pest population. However, some ladybug species, such as the Epilachna varivestis, may eat plant leaves and become pests themselves. It’s best to use Cucujoidea coccinellidae.

Use Organic Pesticides

Mineral oils, neem oil, and other organic sprays like citronella can help remove pests with minimal risks to the aquaponics system. However, they have to be used with caution as excessive amounts getting into the water may be harmful to the fish.

Use a Spray Bottle

Pests can be manually removed using a spray bottle with water from the aquarium. The water can keep the leaves moist, making them unattractive to some pests like mites. However, this method may spread the insects to other parts of the plants and may not be very effective in removing them.

Use Sticky Traps

Placing sticky traps above the plants can also help capture whiteflies and other flying insects. They may not be able to remove all kinds of pests effectively, but they can help reduce their numbers and pose no risks to your plants.

5. Harmful Microbes Are Growing and Thriving

Many beneficial bacteria are used to make an aquaponics system work. However, as plants are constantly exposed to a moist environment, some unwanted bacteria, fungi, and other microbes may thrive and damage or kill the vegetation.

Here are three types of beneficial bacteria necessary in an aquaponics system:

  • Heterotrophic bacteria that release ammonium ions (NH4+)
  • Ammonia-oxidizing bacteria (AOB) that generate nitrites (NO2) from ammonium ions (NH4+)
  • Nitrite-oxidizing bacteria (NOB) that convert nitrites (NO2) into nitrates (NO3)

Meanwhile, plant and animal pathogens may occur and are somewhat difficult to remove. Stringent biosecurity measures are necessary to prevent unwanted microbes from being introduced into the system. 

Here are some safety measures you can take to prevent unwanted bacteria and other harmful microbes:

  • Buy fish and plants from reputable sources.
  • Employ a separate disinfection system.
  • Set up isolated aquaponics systems to prevent the spread of infection in case of occurrence.
  • Maintain water quality and movement.
  • Conduct microbial testing with qualified professionals or certified laboratories.

6. You’re Not Managing the Water pH Properly

Water pH is one of the most important yet challenging aspects to maintain in an aquaponics system. Since fish and plants have different levels at which they can live optimally, the pH must be maintained at a level where both can still survive.

Biological and chemical processes occurring in an aquaponics system inevitably alter the pH of the water. For instance, nitrification, which is an essential part of the system, naturally decreases the water pH. However, drastic changes in the acidity or alkalinity of the water can kill off the fish and plants.

Plants are also unable to absorb certain minerals or nutrients if the pH gets too high or too low. Therefore, various methods must be employed to monitor the water pH and keep it between the ideal range of 6.8 to 7.0. A range of 6.4 to 7.4 is still acceptable for most plants and fish.

Nitrifying bacteria work best at pH levels over 7.5 and stop working when the levels drop below 6.0. In such a case, ammonia and nitrates are broken down into nitrogen, and the water pH rises, leading to health risks among plants that thrive well in a slightly acidic environment.

The water pH must be checked daily. If it drops below 6.5, you may perform interventions by adding bases, such as calcium hydroxide (Ca(OH)2) or potassium hydroxide (KOH). If the system’s pH appears stable or increases for a couple of days, there may be some problems that need to be addressed immediately.

One of the reasons why the pH doesn’t drop is that there may be an excessive amount of organic matter that has to be removed. Another possibility is denitrification or the conversion of ammonia, nitrites, and nitrates into nitrogen. Cleaning the filter tanks twice a week almost always fixes or prevents this issue.

7. You’re Using Treatments Toxic to Plants

As discussed, some essential or trace minerals and nutrients needed by plants aren’t readily available in an aquaponics system. That’s why farmers use treatments that would supplement the amount required by the plants to grow their best.

However, poor judgment or failure to recognize the real issue may result in inappropriate solutions leading to water contamination. For instance, plants display similar signs, such as yellowing or browning of leaves or stunted growth, for shortage or excess of various components for its growth.

Water testing is necessary to determine the actual cause of the issue. Home water testing kits are expensive and not comprehensive, discouraging many people from starting aquaponics as it’s a rather costly farming venture.

Nonetheless, this process is necessary to correctly identify what mineral or nutrient is lacking and more or less provide an estimate as to how much needs to be added. Too little would defeat the purpose of adding the mineral as it can delay plant recovery.

Meanwhile, excessive amounts of products added may also be detrimental to the system. For instance, too much iron will turn the water red, while adding too much phosphorus can trigger an algal bloom that can significantly reduce the amount of dissolved oxygen and cause pH level fluctuations.

Reduced concentration of DO in the system can lead to fish death, contaminating the water and eventually affecting the quality of growth of the plants. It’s possible to manage green algae, but it takes time, effort, and patience, adding to the already tedious process of maintaining an aquaponics system.

Some safe treatments for plants, such as organic sprays or mineral oils against pests may be harmful to fish when they get into the aquarium. When the fishes die from such exposure, it can lead to a buildup of unwanted organic matter that can also be fatal to the plants.

8. You Have a Defective or Dirty Filtration System

Plants benefit from minerals formed from fish waste and other biochemical processes that occur in an aquaponics system. However, excess amounts of solids can form on plant roots and prove counterproductive if they’re not filtered out properly.

A defective or dirty filtration system causes this buildup. Nonetheless, cleaning the system too often can also be bad for the plants as it’ll reduce the amount of nutrients and minerals available to them. Enough time is necessary for the solids to decompose and release the nutrients needed by the plants. Therefore, it’s necessary to clean the filtration system only once or twice a week.

Excessive feeding can result in leftover food and debris that can contaminate the water and clog the filter tanks more quickly. Farmers must remove excess fish food 20 to 30 minutes after feeding. A working filtration system can deal with those that are too difficult to remove.

With the amount of work it has to do, the filtration system must undergo routine checkups to ensure that it’s in excellent working condition.

9. You Have an Unstable Power Supply

A power supply is probably one of the most important components of an aquaponics system. Several components of the system need electricity to keep operating.

Some of these electricity-dependent components include:

  • Filtration systems
  • Water heater and cooler
  • Air and water pumps
  • Lights

Biofilters and solid filtration systems are vital parts of the aquaponics system to control the environment and remove as many unwanted elements as possible. An unstable power supply can lead to a disruption in the process and can prove fatal for both plants and fish.

Air and water pumps are also critical components to promote the circulation of dissolved oxygen and other nutrients between the fish tank and the plant tank. It’s impossible to do so manually, so it’s highly necessary to have a backup power supply or generator in case an interruption occurs.

As seasons change, it’s important to use water heaters and coolers to maintain the optimum temperature for chemical reactions to occur and for plants and animals to survive. Artificial light may also be necessary during seasons when there isn’t enough sunlight.

10. You Have Poor Water Quality

Maintaining good water quality is a challenging but vital part of an operational aquaponics system. The overall health and yield of plants and fish largely depend on how well you can regulate the water quality.

The process is pretty tedious work for beginners in aquaponics. However, mature systems only need regular and routine checks to ensure that irregularities are properly addressed and prevented from escalating into more severe problems.

Things to Monitor in Your Aquaponics System’s Water Quality

Below are water standards that aquaponics farmers need to monitor:

Water Source and Components

There are numerous water sources to choose from when setting up an aquaponics system. However, there may be several issues with the quality of the water. That’s why it’s important to check the water chemistry and ways to remove unwanted elements or contaminants.

In tropical areas where there’s plenty of rain, rainwater is a great source. However, its storage can be a problem as you’ll need a huge volume of water for the aquariums. Also, the chemical components of rainwater can vary at different times of the year.

Tap water is a pretty abundant and convenient source, but its chlorine content can be harmful to fish and plants. It’s also not readily available as you need to let the water sit for a couple of days to release chlorine gas before it can be safe to use in an aquaponics system.

Water from deep wells is an excellent source as it contains some naturally occurring minerals that your plant may also need, such as iron and magnesium. However, it may also contain some harmful microbes, algae, and toxic substances.

Regardless of the source, it’s always important to check the components of the water before introducing it to the aquaponics system.


The ideal water pH that would allow plants, fish, and beneficial bacteria to work and thrive well must be maintained between 6.8 to 7.0. A good rule of thumb is to monitor the pH daily to avoid any drastic changes that may be difficult to remedy quickly enough.


Certain plants and fish species have different temperatures at which they function and reproduce best. That’s why studying what kind of fish and plants to use together in an aquaponics system is necessary. It’s best to pair those that have the closest ranges.

In general, since water temperature can affect chemical reactions and overall plant and fish growth and health, farmers must maintain it between 70 and 85 °F (21 to 29 °C). During summer and winter, adjustments must be made using water coolers or heaters to ensure that the system can continue running smoothly.

Total Ammonia Nitrogen (TAN)

High levels of unionized ammonia (NH3) are toxic to fish and could eventually affect the plants in an aquaponics system. Since the system has limited space and water, it’s easier for the compound to reach toxic levels.

It’s best to maintain the level below 1ppm. Although plants can serve as natural filters for toxic ammonia, you must regularly monitor and measure the total ammonia nitrogen (TAN) using an ammonia calculator app.

I’ve also posted an article about why your hydroponics plants may be dying – check it out!

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.

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