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5 Mistakes In Aquaponics That Make Your Plants Die

Aquaponic systems are essentially very simple but if you are not familiar with aquaponics there are some problems that can cause quite a headache.

However challenging they might be most of problems are caused by lack of knowledge and experience.

If you are aquaponic practitioner you have surely come across some of them.

What is common for most of the problems is the fact that plants are expecting perfect conditions to give us the maximum.

In aquaponics it is quite easy to achieve this perfect environment if we do all that is necessary.

Here, we’ll focus on several crucial and most often problems and challenges you might come across when building and running aquaponic system.

We’ll show you how to overcome them and save a lot of time and energy.

Aquaponic system start and pre-planting water circulation

After you have designed and built your aquaponic system it is essential to cycle the water.

Without proper water cycling you will not be able to create necessary environment for your plants.

In the process of water cycling all essential bacterias and microorganisms are created that will later support the most important processes in your system.

Aquaponic system can be very sustainable system that you can run indefinitely if you start it the the right way. Good start is enabled with water cycling before planting first plants in growing medium.

In this startup process you will have to add very small amount of ammonia to the fresh cycling water that you have put in your system.

When the water is cycling and circulating, after some time first bacteria colonies will start to develop in your growing medium.

For this startup cycling process you will need to let the system circulate water without any fish and plants and after some time (usually in 3 to 6 weeks) your system will be ready.

At this point you will be able to add fish in your system without fear that ammonia might kill it.

Also, after cycling is completed, you will be able to start planting vegetables you want to grow in your growing medium.

If your aquaponic system did not circulate enough and you don’t create enough bacteria that will dissolve ammonia, you will not have functional system.

Your fish will accumulate ammonia that will not be dissolved in growing medium and this might be very dangerous for plants and fish itself.

This problem, the lack of useful bacteria in soil, is also starting to be very evident even in traditional soil farming.

This is due to a large amount of chemicals that people are using in farming and that are polluting the soil and water. These chemicals are killing diversified world of micro-bacteria without which further natural processes of fertilisation and nutrients creation are not possible.

When this natural environment in corrupted, in the soil, it is extremely hard to fix the problem.

For this reason it usually takes 3 to 5  years to clean soil from all the chemicals and to re-enable creation of environment for useful soil bacteria.

This is how long it usually takes to get certification for organic food production when you start growing organic food on contaminated soil.

When we consider aquaponics as the solution for this problem we find that aquaponics is almost perfect for achieving this naturally balanced environment.

Mainly because it is closed recirculating system that enables you to fully control all aspects and factors.

To have healthy and well fed plants you need to focus special attention to water circulation as the first step.

This will enable you to eliminate most of the problems that might occur later on.

Pest control in aquaponic systems

Pest control in natural and organic food production can deliver many surprises.

It may seems that it is quite easy to achieve good organic pest control but experience can deliver many obstacles and challenges.

It is widely accepted that healthy plant is the first and most important condition of pest control.

But this is surely not enough.

If you don’t take this problem seriously you might run into a trap.

When you first notice problems in your aquaponic system and garden it is usually already too late and all you can do is control the damage.

The aquaponic systems are closed systems in which the water is circulating between fish tanks and plants.

For this reason you need to be aware that everything you might use for pests control on your plants will eventually end up in the water and in fish tanks.

Although there are many different organic pest control solutions for your plants, you need to know that most of them are very dangerous for the fish and it is not advisable to use them in aquaponics.

You need to be very careful.

One of the safe organic pest control resources you can use in your aquaponic system are predatory insects. The most useful and efficient is “Bauveria bassiana”.

One of the safe organic pest control resources you can use in your aquaponic system are predatory insects

You should have in mind that predatory insects are used for prevention but they are useless for fighting the problem if they have already occured.

To prevent most of insect problems it’s good to setup insect screens in your greenhouse.

Greenhouse insect screen

You can also use pheromone traps.

It’s a type of insect trap that uses pheromones to lure insects. Pheromone traps are very sensitive, meaning they attract insects present at very low densities.

They are often used to detect presence of exotic pests, or for sampling, monitoring, or to determine the first appearance of a pest in an area.

The fact that pheromone traps are highly species-specific can also be an advantage, and they tend to be inexpensive and easy to implement.

However, it is impractical in most cases to completely remove or “trap out” pests using a pheromone trap. Some pheromone-based pest control methods have been successful, usually those designed to protect enclosed areas such as households or storage facilities.

In closed growing spaces the most spread insects are cabbage whitefly (Aleyrodes proletella) and thrips (Thysanoptera).

But, the most important thing is to notice problems in the beginning because if you allow them to reproduce it will be very difficult to fight the problem organically.

The cabbage whitefly

The cabbage whitefly lives on the back of the leaves and it damages plants by sucking plant juices and by excretion of metabolic waste.

Cabbage whitefly

This insect is mostly attacking tomato, paprika, cucumber and flowers and is very often seen in closed growing spaces.

It has 10-12 generations per year. Having in mind that it usually develops in closed spaces with perfect growing conditions if you do not prevent or fight this pest you might have pests of all growing stadiums in your greenhouse.

As the consequence of this pest activity, the plants will grow slow, the yield will be smaller and of lower quality.

If you allow cabbage whitefly to spread in your greenhouse it will develop large population and it might be very challenging for you to get rid of them for two reasons:

  • this species develops very fast resistance to different chemicals and insecticides  
  • they reproduce very fast and you might have all growth stadiums in you greenhouse that all have different resistance factors

When fighting cabbage whitefly you need to notice them on time. For this purpose it is good to use sticky surfaces that you can hang around greenhouse. As soon as you discover these insects you need to act.

The Thrips

Thrips (Thysanoptera) are minute (most are 1 mm long or less), slender insects with fringed wings and unique asymmetrical mouthparts.


Different thrips species feed mostly on plants by puncturing and sucking up the contents, although a few are predators.

Many thrips species are pests of commercially important crops.

A few species serve as vectors for over 20 viruses that cause plant disease.

Some species of thrips are beneficial as pollinators or as predators of other insects or mites. In the right conditions, such as in greenhouses, many species can exponentially increase in population size and form large swarms because of a lack of natural predators coupled with their ability to reproduce asexually, making them an irritation to humans.

Thrips are attacking more than 150 different plants and it loves warmer climate.

Larve and grown insects are feeding with plant juices. They drill leaves and insert their saliva into plants. The air that is filling empty cells is giving recognizable silvery colour to the leaves.

It can lower leaves growth by 35% and it reduces the quality and the quantity of yields.

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Fighting pests naturally in aquaponic system

The first and last link in pest control is healthy plant itself.


Well, healthy plants have a lot of potassium in their leaves.

Potassium in plants works in such way that it block insects in some way as most of them do not like potassium. Also, healthy and potassium rich plants are very durable to all the consequences of pest activity.

Another reason why healthy plants are the best pest prevention lays in the fact that healthy plants are hormone rich. Hormones affect pests the same way as potassium. Pests do not like it and plant has a lot more power to fight negative effects of pest influence.

We should not forget that in aquaponic systems we are growing plants in closed systems that are not natural. For this reason, to have healthy plants that are more durable to pests influence, we need to pay attention to every detail and to provide all necessary nutrients to our plants so they can be potassium and hormone rich.  

Hungry plants in aquaponic systems

Generally speaking, all plant problems in aquaponic systems begin when we do not provide necessary nutrients to our plants.

Factors that make our plants well fed are:

  • nutrient minerals (micro i macro elements)
  • non mineral nutrients (oxygen, hydrogen, carbon dioxide etc.)

Basic nutritive elements, that play the most important role in plant development in aquaponic systems are very easily delivered to your plants when aquaponic system itself was build the right way.

Nitrogen is one of them. It’s the element that is crucial in aquaponic systems and usually aquaponics systems have abundance of nitrogen.

But, nitrogen is not sufficient by itself, for healthy plant development. There are many other nutrients that are crucial for plants.

If you pay attention, plants will tell you what they need. It is your task to recognize what they are telling you and to know how to react when something is needed.

Other nutritive elements are created by time in anaerobic parts of your system.

Sometimes you can compensate some of nutrient elements with organic and non-organic solutions. For example, the lack of magnesium can be compensated by adding epsom salts to the water.

Related article:  How To Create Great Aquaculture Environment

If you know how all the elements influence on plants and if you know how to compensate the lack of some, your plants will grow healthy.

But don’t worry. If you are not an agronomic expert you should always know that plant will show you symptoms that can easily point to the right direction of what nutrients it is missing or lacking.

It is good to know that besides nutrient deficiencies you can also encounter nutrient abundance that can also be harmful to you plants.

When your aquaponic system have a lot of specific nutrients it can create toxic environment for your plants and for your fish also.

For this reason it is important to create true ecological balance and only then you will be able to get the best results.   

Power of hydrogen and aquaponic systems

Since aquaponic systems are closed water circulating systems, water pH value is one of the most important factors of success. It is important for development of:

  • Fish
  • Plants
  • Microorganisms

pH is a measure of the acidity or alkalinity. In the pH scale, pH 7.0 is neutral. Below 7.0 is acidic and above 7.0 is basic or alkaline.pH is a measure of the acidity or alkalinity

There are some contradictory opinions about what pH value is the best for aquaponic systems.

You have to make balance because fish, plants and microorganisms demand different Ph values for different grow stadiums.

Fish has one ideal pH value for perfect development. Microorganisms have another and plants will absorb different nutrients on different pH levels.

If you do not make perfect balance you will not have healthy aquaponic system. This is why water pH level is crucial for every aquaponic system.

Based on my experience, ideal pH value for aquaponic system is between 6.2 – 6.4.

This value should satisfy all important demands but there is one potential problem.

When pH is 7 this makes water neutral. Or should we say 7 is neutral pH value. Most of public water sources have pH value 8 and this makes water quite unsuitable for aquaponic system.

To get ideal value of 6.2 – 6.4 we need to add acid to the water to make it suitable for usage in aquaponics.

Aquaponic nitrification process lowers water pH values but this is usually not enough, you need to additionally make water pH value lower. This is especially important in the beginning when aquaponic system is still young and not all microorganisms are created.

WARNING: Do not listen to advices that say that you should lower water pH value with lemon acid and vinegar. Lemon acid and vinegar will lower pH value of water but they will also destroy all the bacteria that is crucial for aquaponics. Vinegar will also make abundance of chloride that can not be used in aquaponic system and will make your water toxic for plants and fish.

The best way to lower pH value of water is with some acids based on:

  • nitrogen
  • phosphorus
  • sulfur

With these acid compounds not only that you will lower water pH value but you will also add nutrient minerals to the water that are important for your plants.

Another important thing is to notice that pH affects nutrients available for plant growth.

In highly acidic soil, aluminum and manganese can become more available and more toxic to plant while calcium, phosphorus, and magnesium are less available to the plant.

In highly alkaline soil, phosphorus and most micronutrients become less available. Check the picture bellow to see different pH levels and nutrient availability.

ph and nutrient availability

When we have this in mind it is evident that for the best results pH levels need to be dynamic and should not be fixed all the time.

But, as majority of water sources available have much higher pH levels (around 8) though process of lowering pH levels we are practically enabling plants to absorb all important nutrients.

Also, if you have water sources with high pH value and you want to maintain ideal pH value of 6.2 – 6.4 you might get into problem as this would require substantial quantities of acid.

This can influence aquaponic system rentability. For example, if you use nitrogen acid you will add very small amounts of it periodically. But, annually this would require substantial quantities of it.

However, there is solution for this.

I have tested aquaponic systems with water pH value of 6.2 and 7.

It is much easier to maintain water pH value of 7. You will need 10 times less nitrogen acid and results will be practically the same.

But you should take notice that this is my practical experience and for your particular situation it might not be the same.

Depending on your water sources and pH value you might get different results.

For all the reasons mentioned, it is very important to notice that pH value is crucial for your aquaponic system and wrong pH management can kill your plants and your fish.

Water filtration in aquaponic systems

There are two types of water filtration in aquaponic systems:

  • chemical filtration
  • mechanical filtration

Chemical filtration is microbiological conversion of ammonia that depends on the balance of aquaponic system elements.

To get the best results from your aquaponic system you need to balance:

  • growing medium as biological filter
  • quantity of fish
  • quantity of water

This is the greatest challenge for any aquaponic system designer.

If you get help from experienced aquaponic system designer you will not have to worry about these elements. But, if you are just starting you’ll find that this can be the major problem.

There is no simple formula that can give you the answer to this question but there are some resources online that can help you solve this problem. This is mainly because the calculation depends on:

  • type of plants you are growing
  • grow stadium of your plants
  • quantity of water in your system
  • quantity of fish in your system
  • piping and water circulation etc.

The best teacher is experience itself.

Related article:  Aquaponic systems for beginners

In my 6 years long aquaponic journey I have made a lot of calculations for my aquaponic system but also for systems that I’ve been hired to design.

In this process I have come to many different formulas that help me design balanced aquaponic system. I’ll get to these in my next posts as this subject by itself is too complex and too important and it deserves much more attention.

If you get all the elements right in your aquaponic system you’ll know it by simply tracking basic system and water parameters.

All the processes that are happening in aquaponic systems are simply a copy of natural processes. But, proper functioning of your aquaponic system is your responsibility as here everything depends on you.

Second type of filtration is mechanical water filtration.

Large particles in water circulation can create problems that will cause your plants to die as they will not be able to receive necessary nutrients. These problems are caused by:

  • clogging of watering parts (pipes, nozzles, sprayers etc.)
  • accumulation of ammonia in the system

Aquaponic system need to be as automated as possible. Ecological system of nature is truly automated but it’s elements are not visible as it is perfect system.

Aquaponic systems need to be balanced and perfected by us by controlling and automating as many factors as possible.

If you ignore some elements it may happen that in one moment you get too many problems and it gets harder to find true cause of all these problems.

For the best results you need to pay special attention to your piping and watering parts as well as to the transfer of water from fish tank to sump tank. This is because majority of large particles are created in your fish tank and if you don’t stop it from getting into you system at this point it might cause many problems down the line.


As you have seen, aquaponic systems are not as easy and problemless as it might look.

There are many challenges that you are facing if you want to design and build great aquaponic system for the best results and yields.

But, fortunately each and every problem have a solution and in reality the best advice is to pay special attention to design process as majority of problems can be avoided by simply following the rules of aquaponics in design and building phase.

I’ll get back to some of the specific problems and solutions in my next posts so stay tuned.

I hope you find this article useful and helpful and I appreciate any comments or suggestions you might have.

So feel free to leave any comment or simply write me an email.

And in the end, if you like this article please do share it with your friends.


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