Aquaponics pest control can be tricky. in this article you will learn how to manage the pest population without problem for the ecosystem.
Aquaponics friendly pest control
What you will learn in this article:
  1. Aquaponics pest control consist of managing living populations
  2. Weak and young plants are most subject to aquaponics pest
  3. Detect pest invasion by checking leaves, look for insect poop and inspect at night
  4. Work with biodiversity
  5. Use safe aquaponics pest control methods
  6. Give infested plants to your fish for a free clean
  7. Avoid commercial pesticides
  8. Design commercial systems with a modulable water flow
  9. Remedies used by others

What is aquaponics pest control?

“Pest control” is the action to regulate the population of living creatures competing with humans. In fact, those animals compete for food, they consume our crop. Indeed, as they are not desired, they are often qualified as “Pest”. However, In aquaponics we understand that we are working with an open ecosystem. Therefore it is our mission to offer good conditions for the crop. But we understand that all animals have their place in the ecosystem. Hence, our work will be to “manage the population”. As a result, the term “pest” is not the best to qualify those animals. However, in this article I will keep using it so everyone understand what we are talking about.

What plants are the most subject to pest attack?

Let’s be clear, no plant is safe from pest invasion. However, some plants are more sensitive than others. In fact, the weaker plants are the first to suffer from insect invasion.
  • In this category we have the crop arriving at the end of the season. Indeed, they will be easily reached by insects. In fact it’s not such a problem to share those ones with nature since they are going to die anyway.
  • The other type is more critical, they are the young plants with thin and tender leaves, Insects love them. Actually you will notice that even in well developed plants, the new leaves are often the first to be attacked. So keep an eye on those.

How to detect a pest invasion?

Most people detect a pest invasion when they see heaps of pest or when the crop is already damaged. However, a good aquaponics grower enjoys to observe the ecosystem everyday. As a result he is able to see the pest population increasing before a major attack occurs. So here are the 4 things to look for:


Pest holes on chili

Check the leaves of your plants and see if you can spot holes. Of course, one or 2 are normal and acceptable. But if you see the holes increasing, it probably worth to check closely.


Caterpillar poop

Check the plants and see if you spot some dark green dots, those are caterpillar poop. Indeed they are generally easy to spot as they form a nice contrast with the leafy green. So if you see a lot of them, you know that a caterpillar is nearby.


Butterfly over aquaponics tomato plants

This one is straight forward. Observe and try to spot the insect itself in your aquaponics grow-bed.

Night session


It is something I love doing. Check your aquaponics grow-bed during night time. You will see a totally different population of animals. During daytime most little creatures are hidden. They hide from sun and from classic predators such as birds. By night insects are out, slugs and snails are crawling around. This is the best time to check on them.

Under rocks…

Slug under stone

Look under stones, boards, bell siphon, large leaves or any material placed on your grow-bed. You may find slugs and insects. If your grow-bed contains a small media, you can add a few flat stones and check underneath some time to time.

Common pest in aquaponics

Among the most common aquaponics pest we have:


Aphids on aquaponics plant

Aphids are small insects sucking the sap of the plants. They sometimes live in symbiosis with ants who protect them. Aphids can multiply extremely fast. One single individual can produce a colony as they are able to reproduce by “parthenogenesis”. Plants can survive with a few aphids. But if the number increase they will stress the plant and eventually kill it. In aquaponics we often find them on leafy plants such as broccoli, lettuce…


Caterpillar on tomato leaf in aquaponics

Caterpillar are butterfly or mouth larvae. They look like a worm and climb on the leaves to consume it. A caterpillar can consume up to 27000 times it’s weight of leaves within it’s lifetime. Llifetime that is relatively short (few days) by the way. In aquaponics they can create a real damage on the crop. Each species specializes into a specific crop type. We often see them on the tomatoes, chili, zucchini, capsicum plants or even lettuce…



Whiteflies are common on tomatoes. They affect the plant as they feed on it and inject a toxin. Unfortunately they can also carry viruses as they go from plant to plant. Bemisia whiteflies are often found in greenhouse. they can be challenging to regulate.

Slugs and snails


Slugs and snails are common garden crawlers. They enjoy the aquaponics system and the small slugs sometimes hide below the rocks. Slugs are more active by night but you can often spot them below rocks during daytime .



Fungus are not rare in aquaponics. Most of them are beneficial. However, some species may affect the poorly designed aquaponics systems. Indeed, most fungus require a moist environment. I see too many aquaponics systems with a wet media on the surface. It is important to keep the first 3 cm dry to avoid algae and fungus development.


Nematodes root knot small

Some people add nematodes to the “pest” list. It is true that in a classic garden some can attack the weak crop. However, in aquaponics most worms are beneficial. They break down the organic matters into smaller particles edible for bacteria.

Birds, rabbits, possums, rats and squirrels

Zucchini attacked by birds zoom

Zucchini attacked by birds

Those are large animals. They can cause serious damages to your crop. As we will see below, physical barriers are probably the most effective way to keep them away from your grow-beds.

Common natural predators useful for aquaponics pest control

Here is a list of common natural predators that you will be happy to see in your aquaponics grow-bed. Feel free to add insect hotels to offer them the best habitat.


LadybirdLadybirds are very nice to have in aquaponics. The kids love to see them. But Ladybirds are not only pretty, they are also very useful in aquaponics. They attack aphids but the real predators are the larvae. The ladybirds larvae consume aphid after aphid. They can save your entire grow-bed from an aphids infestation.

Praying mantis

Praying MantisPraying mantis are like aliens. They are the strangest creatures. I could spend hours watching them. They hunt all kinds of insects and are helpful in aquaponics. If you see some in your grow-bed you can leave them and be careful to not squash them when you harvest your crop.


Hoverflies or syrphids

Syrphid - Hoverfly on aquaponics tomato flowersSyrphids also known as hoverfly are unique. They look like a little wasp as they are strapped yellow and black. They generally fly over your crop and inspect the leaves looking for prays. Syrphids consume mainly small insects. Like the ladybirds, the larvae are more efficient than the adult to consume aphids. They catch the insects one by one and suck their blood. they can clean a whole plant in no time.

Black hornets

Black hornet

The Black hornet is a peculiar insect. They fly around the crop and when they spot a pest insect such as caterpillar or aphids, they spawn their eggs inside. It may seem completely crazy but the black hornet larvae are growing inside their host and eat it from inside. Once the larvae are large enough, they burst out of their dead host. Hundreds of baby black hornets can spring from one caterpillar. They then become an army of soldiers looking for a new host insect.



Lacewings are also interesting insects to have in aquaponics. They eat small insects such as aphids and insect eggs. they lay their own eggs on a long silk stick raised a few centimetres away from the leaves to keep them away from predators. 


Bee on aquaponics tomato flowerBees are great to have in your garden. They don’t really help to control other pests but they fertilize the crop. Bees are needed in order to get fruits and they are a symbol of life.



DragonflyDragonflies are amazing predators. They consume a large variety of insects and are great to watch. The larvae are aquatic. They can also be useful in the fish tank. Your large fish may eat them. However, if you have little fish fry (new born) in the tank, the ladybird larvae will get their share of the menu…


Spider on aquaponics silverbeetThere are thousands of spider species. Most of them are harmless for humans and they will be a great help for your aquaponics pest control. Take care of them and learn to like them.




Relation pest / predator in aquaponics

Pest - Predator table in aquaponics

Two aquaponics pest control approaches
When it comes to health treatment we can generally see two approaches. I am talking about health treatment in general because the following is true for plants, animals and humans…

1. Give them a pill

The first approach is to treat the symptoms. This is what doctors do when they give you a pill to minimize the symptoms of a disease. They tell you: “You have cancer? OK, take a pill every day and don’t change anything to your habits. if everything goes well you will live for 5 more years. And yes, you will have to deal with the medicine side effects”. Let’s be honest, this is not solving the issue and side effects are sometimes the cause of death.

2. Treat the cause

The second option is to treat the actual cause of the problem.
In this example, the doctor will try to find out why the person fell sick and improve the lifestyle of the person. this includes physical activities but also dietary, stress… By removing the cause of the problem, we avoid the disease.
So let’s go back to our aquaponics crop now. Can nature show us the way? Can we compare our aquaponics ecosystem to a naturally occurring production system?
Yes we can! A perfect example is a forest. When you walk in a forest what can you see? You can see a multitude of plants, trees, insects… all living together. What is very interesting to realize is that they generally look very healthy. You will find dead trees here and there but you rarely find sick trees. Why is that? Why do farmers have to spread pesticides while in a forest, everything is growing healthy?
Do you have an idea? OK I will leave you 1 minutes to think about it…

The key to aquaponics pest control is biodiversity

OK here we go: In a natural ecosystem like a forest, the biodiversity is everywhere. If you look closely, there is not only one type of plant but a multitude of species. This is also true for the trees and all the animals living in the forest. It makes a huge difference with an intensive agricultural field. Let’s take the example of a corn field. The only living creature that the farmer allows is the corn plant. We call this technique “mono-culture” as only one species is grown. Furthermore, the farmer uses pesticides to kill all other living creatures.

Why biodiversity makes such a difference?

If you are growing only one crop, you don’t need long for the adapted “pest” to arrive and spread on your whole crop. In fact, the “pest insect” will find a quantity of food and no predators. Therefore it can quickly multiply and devastate the entire crop.
In a forest or in permaculture, the different species grow together. When a “pest” reach your grow-bed, it has few chances to find the targeted species. Also, the other plants are acting as fences. their smell and shapes disorientate the insect and slow or stop the pest progress.
Furthermore, the multitude of plant species offer a wide variety of environment. This is exactly what predators need to live in and remain in your grow-bed. Therefore, we have more predator diversity ready to protect your aquaponics crop. In permaculture it is becoming very common to add insect hotels. We can also use this technique in aquaponics. When I design wooden aquaponics grow-beds, the space between the wood sleepers is actually acting like an insect house. I often see “bugs” and lizards living in it.
Space between sleepers in growbed

Space between sleepers in growbed

Does it mean that your crop will be 100% safe from “pest attack”?
Mmmmm No! We must apply a good philosophy here. In order to harvest sustainable, healthy and tasty food, We are happy to share a bit with nature. It generally doesn’t go over 20% of our crop and fortunately this is enough to avoid the use of pesticides. If you are not ready to lose few plants, you will find here below a list of aquaponics pest control techniques usable to minimize this loss.

Safe aquaponics pest control methods

Physical barrier

You can keep your crop safe from a quantity of predators by placing a physical barrier around it. Nets (insect of bird nets) are one of the most effective protection. Nevertheless, they are not always the most aesthetic option.
Chicken mesh is also a good option to stop access to the larger predators such as rabbits, dears, rats, squirrels…

Light on top of fish tank

In aquaponics we are working with a fish tank very close to our grow-bed. Let’s take advantage of it 🙂
You can place a little light just on top of the water during the night to attract insects. They will circle around and eventually fall into the fish tank. Your fish will be happy to find a fresh source of proteins and your plants will grow better 🙂


You can find a multitude of traps to protect your crop.
Insect traps are generally attracting insects with pheromones (sexual hormones).
I don’t need to detail the famous bier trap for snails and slugs any longer. You will be able to get them from any good garden shop.
Rat traps are also very efficient.

Fake predators

Plastic predator (snake)

The principle is to use them as you would use a scarecrow. I personally use plastic snakes. Others use fake spiders or owl. The trick is to move them from time to time.

Fake fruits

Tomatoes fake plastic
I sometimes add red plastic balls to my tomato plants at the beginning of the fruit season. Birds are coming and picking in the plastic balls. Then they lose interest when the real fruits are maturing. Well, that’s the theory 🙂

Copper wire / tape

Snails and slugs don’t like copper and they generally avoid to crawl on it. You can surround your aquaponics grow-bed with copper wires or copper tape. It will reduce the quantity of slugs and snails on your crop.

Insect hotel

As mentioned above, many materials can be used as an insect hotel. The beauty of those insect houses is that they will keep the useful predators around for you. It’s an army of insect soldiers working to defend your crop.

Waste management

A mature aquaponics system has tendency to look like a real jungle. Some people like to live the old leaves into the system as it adds more nitrogen. Personally I believe there are enough organic matters to fulfill our plant needs. I would advise to remove old leaves and rotten fruits as they may attract pest.

A little trick to get rid of pest insects 🙂

Yes you may have a peak of an insect population such as aphids. If you leave the plants alone, most will survive and natural predators will appear as explained above.
However, some plants may not be able to make it. If it’s the case, don’t throw those plants away. A good way to take advantage of this situation is to pull the plant and to place it up side down in your fish tank. The fish will probably be very interested to eat the insects growing. In this case you will close the loop! Insects will become a perfect fish food. Be careful however to not leave the plant too long into the water. If like me you have omnivorous fish, they will surely enjoy the aphids but they may also like to eat the plant leaves…

The reason why you should avoid classic pesticides

Don’t damage your nitrogen cycle

You know that in aquaponics we are working with fish, plants and bacteria. If you spray a pesticide on your plants, the aim will be to get rid of the pest. However, you may observe an impact on the fish. And for sure you will damage your bacteria population. Without bacteria, your nitrogen cycle will stop. As a result, the ammonia toxicity will increase. Unfortunately, this is simply the best way to kill the fish.

A closed system…

Unlike in a classic garden, in aquaponics we are working in a closed system. In the instance of spraying a classic garden, the chemical reach different areas:
-The plants absorb a certain quantity
-Rain and wind will wash the rest and it will finish into the soil.
-With time, part of it will go in the deep layers and evacuate from the garden.
In classic aquaponics, whatever we add to the system will remain into the system. This is great when you add natural elements. However, it’s not that good when you add nasty chemicals…
In aquaponics, if you add chemicals, it can accumulate into the fish flesh or in the veggies. Therefore, you can expect to find most of it in your plate under one shape or another.
I hope you now understand better why I am so reluctant to use pesticides in aquaponics. From my point of view, the aim of aquaponics is to produce healthy and sustainable food. If you consume pesticides with your crop it will not be healthy and may be very harmful.

Modulable water-flow system

After reading the above you may still want to use pesticides. It may be because you plan to grow aquaponics commercially. In this case I recommend a specific water flow design. You see, in aquaponics we normally work in a closed water flow system. If you plan to run a commercial aquaponics farm with DWC, I would recommend a specific water flow design. Conceive it with the option to open your cycle if required. In other words, If you need to treat your plants, make sure you can remove the water without going through the biological filtration and the fish tank.

Some remedies used by others

Here is a list of products qualified by others as “pesticides safe for aquaponics” or “fish safe insecticides”. Please note that I don’t use those products and recommend to stick to the practice listed above.
Bacillus thuringiensis: This insecticide is composed of bacteria producing a toxin killing caterpillar. The organic standard accepts this type of product. However, there are no study on the impact of this product on the whole aquaponics ecosystem. For this reason I recommend to avoid or do some trials with those pesticides as they could make the situation way worst.
Natural oils such as nem oil are effective to kill most pest. it must be diluted and sprayed on the foliage. It’s natural as it’s made from Azadirachta indica, an Asian/Indian plant.

Home made spray pesticides

There are tons of home made pesticides considered organic recipe used around the world. Let’s be honest, I am not an expert of those but I have tried a few with mitigated results. The most common home made sprays are:
  • Garlic and chili spray: can work to a certain extend
  • Vinegar and salt spray: be careful as it can also affect your plants
  • Soap / dish washing spray: can be efficient but make sure to not spray the media.
  • Diatomaceous earth: The effect of those extremely fine particles on human are still unknown. It could be dangerous to breath it. So be careful with this one.
Tomato leaf spray, Tomato contains a toxin, the tomatine. When you chop tomato leaves and add them to a bucket of water, the toxin dilutes into the water. You can then spray this liquid on your crop to manage the bugs invasion. I found this interesting to use on aphids and fungus.

Final thoughts

There are 2 ways to approach pest control in aquaponics. You can focus on the pest and use the strongest destructive weapon to get rid of it. Or you can have a more holistic approach and take care of your whole ecosystem. Working with nature to balance populations. In conclusion, If you are a nature lover, I know that you will develop the good mindset and succeed in aquaponics pest management.

You will probably be interested to discover my six steps to build and manage an Aquaponics system. Click here to access for free! Thanks and good reading 🙂