Hydroponic Pest Control: How to Protect Your Plants

When you’re using hydroponics to do your gardening, you don’t have the same risk of pest infestation that you do when outside. However, you probably still have some concerns about protecting your plants from pests. It’s a good thing to be vigilant, but it’s even better to prevent a pest problem before one happens. So here’s what you need to know about hydroponic pest control:

The most common pest problems in hydroponics

If you want to control pests, you first need to know what you could be dealing with. Here are some of the pests that you’re most likely to find if you’ve got pests in your system:


A lot of people are familiar with aphids from school lessons, and here you thought you were done with them. But they do infest hydroponic systems, especially when your plants have too much nitrogen in their food source. They’re usually found around the plant stems and these little guys can be either black, green, or grayish/tan.


Whiteflies can be tricky, but you can spot them pretty easily. They look like tiny white moths (about 1mm long), and fly away as soon as you’re about to catch one.

Spider Mites

Spider mites are even smaller than whiteflies, at under 1mm in length. And they’re definitely one of the most dreaded infestations of a hydroponic system. They do look like tiny spiders, but since they’re so small they can easily escape notice until an infestation gets way out of control.

Fungus Gnats

Fungus gnats are another tricky pest, since the grown gnat isn’t harmful but the larvae is. You’ll find the pest larvae eating at roots, which can bring on bacterial infections pretty quickly. 


Thrips, like aphids, can turn leaves yellow or brown because they suck the nutritients out. They’re a little bigger at 5mm, but still hard to spot. They’ll look like small, black dots on the upper sides of leaves.

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Avoid things that ‘invite’ pests into your growing area

There are certain ‘good practices’ that can help reduce the chances of a pest making its home in your hydroponic system. Fortunately, a lot of these practices involve a little know-how, and a bigger dose of avoidance. That means one of the best things you can do is avoid introducing opportunities that appeal to pests.

Don’t go in dirty

Before you enter your growing area, you should be wearing sterile (or at least clean) clothes. All kinds of bacteria, pests, and other contaminants can cling to our clothing totally unnoticed. Even if you don’t think there’s anything there, just don’t risk it. A pest problem is a high price to pay for skipping 2 minutes to get ready to enter your growing area.  You’re not done yet though, your tools and anything you bring into your growing area needs the same care.

Basically: don’t bring anything into your growing area that isn’t clean and contaminant free.

Give your system a sterile start

If you’re setting up your system, or doing a little work on it, see the tip above. Even fixtures, vents, tanks, and any other gear needs to be cleaned before they’re introduced into your growing area. Period.

Checking the quality of the seals around your growing area is important, too. While you want a well ventilated area, you don’t want a free for all for pests. Make sure there isn’t an issue with seals on windows and doors to outside areas (especially when your growing area is close to outside vegetation). 

Outside Materials

Pests can crop up from some sneaky places, and the materials you introduce into your hydroponic garden are an unassuming hiding place. The pest home that we inadvertently bring into our hydroponic systems?

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Growing medium.

Look, this isn’t to create a scare campaign because the truth is most growing mediums are perfectly sterile, and safe. But there are some things to look out for. If you’re getting an organic growing medium, such as coconut or rice husk, pay special attention. These mediums can harbor pests, so they need special treatment. Make sure that your growing medium has been sterilized, put through treatments to eliminate pests, and has some credible backing behind those claims.

New Transplants (take care)

Whenever you’re planning on adding transplants into your system, you need to be careful. Outside plants can carry bacteria, fungi, diseases, and pests. To combat these risks, you need to get any transplants from a clean, well maintained place you can trust. And before you go transplanting anything just because it came from a ‘reputable’ facility, take the time to examine the plants for any health issues.

The first steps in hydroponic pest control

Pest control can be something you start practicing with at the very start with your hydroponic system. Basically, putting in measures that deter pests is going to be your first line of defense. Here are the best ways to prevent a pest problem:

Watch your humidity

Some pests, like spider mites and fungus gnats, are especially attracted to low humidity and excess moisture in other parts of your system. Keeping your humidity from getting too low (50% is a good level to keep plants healthy and keep mites away), can prevent an infestation. But it isn’t all about your ambient environment. Keeping too much moisture from your growing medium can deter pests, like fungus gnats, from taking up residence (especially if you use rockwool, which they love).

How to identify a pest problem

Even with diligent prevention, you can still have a pest sneak its way into your system. Like any hydroponic set up, you should be examining your plants for problems regularly. That being said, you don’t want to confuse signs of pests with signs of other issues, such as nutrient deficiency or disease. Here’s how to tell if your plants are suffering from pests, or another ailment:


When pests suck the nutrients out of leaves (like aphids do), you’ll notice that the leaves become discolored and often turn a yellow color. This discoloration is centered around tiny holes that the pests feed from, not just generally spread on leaves.


Some pests can leave a signature pattern of spots, whether white, yellow, brown, or black.  If you notice spots, check to see if they’re deposits on the leaves (from eggs, feces, etc), or actual damage to the leaves. If the spots scrape off, you can pretty well bet you’ve got a pest issue.

When you notice these on any plant, check the leaves and stems of other plants to determine the pest and the degree of infestation.

Holes from pests vs burns and lesions:

When you first see a hole or rip, it can be easy to make assumptions. That’s why it’s important to look closer and check out the edges of any holes. Burns should be fairly obvious, as they’ll appear where light and heat sources are close to plants, and show discoloration around any holes or burns.

The pests that are most likely to infest hydroponic gardens are more ‘suckers’ than ‘munchers.’ That means the holes they leave from feeding on plants are tiny, and often raised and surrounded by a more yellow, or whitish area.

What to do when you have a pest?

If you’ve noticed some of the above symptoms of a pest problem, you need get it fixed and quickly. Unfortunately when a pest has already made its way in, it can be difficult to mitigate the issue.  Pests can run through a hydroponic system at a surprising speed, so once one plant is affected the others tend to follow in short order.

Don’t wait to take care of a pest.

If you act immediately after spotting pests, you may be able to spare the rest (or remaining unaffected) of your plants. If you wait, you’re probably going to come home to a garden that’s been almost, if not entirely, infested.

Determine the level of intervention needed:

Some pests can be taken care of by changes to the environment, manual removal, or other methods, while some pests can only be banished with chemicals. Whenever possible, avoid introducing harmful chemicals into your hydroponic system.

More gentle methods of pest removal:

Sticky traps

One of the first things you can do, depending on the pest you’re dealing with is use sticky traps. These work like the other sticky bug traps you’re familiar with, and can be really helpful especially with pests that have short life cycles. Another bonus of using sticky traps is that it can help you identify the pests infesting your system. If you can identify the pests, you can take a more appropriate route to getting rid of them (even if sticky traps don’t eliminate them).

Tip: Keeping sticky traps can be a preventative measure, too. If you see pests caught on a trap you can prevent a larger issue.

Natural solutions

A lot of solutions are marketed for killing pests, but you don’t want to chance killing your plants too. When in doubt, make sure your solution is backed with plant safe guarantees. A solution you can rely on, without a doubt, is Pyrethrin. It sounds very chemically intense, but don’t worry. It’s been given the green light for even certified organic farmers to use, so you know it’s safe. Pyrethrin is extracted from chrysanthemums, and can put a stop to pests.

A good spray down

Oftentimes you can give your plants a good hosing down to start getting pests under control. True, it won’t kill all your pests, but it can disrupt another cycle of reproducing, and it’ll get the bulk of them off your plants.

Hydroponic pest control: The cheat sheet

If you’ve found yourself with a pest problem that quickly becomes an emergency, here’s the cheat sheet you need.


  • Black spots on leaves – see Thrips
  • White or yellow spots – see Spider Mites, Whiteflies, Thrips, Aphids
  • Deformed stems or leaves – see Fungus Gnats, Aphids
  • Deposits on leaves – for silvery streaks see Thrips, small black see Thrips, sticky residue see Aphids, white masses and clumps see Mealybugs
  • Webbing around plants – see Spider Mites

Pest information and treatment


Aphids secrete honeydew, a sticky residue that stimulates the growth of sooty mold (honeydew can also attract other pests such as ants). These creatures such nutrients out of leaves and can leave them looking yellow and crinkled.

Tell-tale signs:

Aphids leave behind a good deposit of honeydew when they’re feeding, so you’re unlikely to miss these deposits. You can usually spot the aphids moving around stems, although they can be a variety of colors.


You can use predator bugs that feed on aphids to control their infestation; ladybugs and lacewings are the most common choices. Safe soap pesticides contain different formulations, but most are safe for plants and deadly for pests. Leaves, stems, or even whole plants that are severely infested may need to be removed. Next, try not to overfeed your plants, as that will increase aphid problems. 

Fungus Gnats

Adult fungus gnats are annoying but not a huge problem (aside from the fact that they reproduce). The larvae are going to be your real issue, as they congregate near and fed on the roots.

Tell-tale signs:

The first sign you may notice is the adult fungus gnats that fly up in masses whenever you disturb a nearby area. The larvae can be found by looking at the growing medium, and turning it over a bit. The plants they feed on start by looking ‘ill,’ meaning they get yellow leaves, look wilted, and seem frail.


First, avoid these guys by trying not to overwater your plants; but if you’ve already gotten to that point, try letting the growing medium dry out as much as possible, to a couple inches from the surface before adding any more moisture. You can catch eggs with sticky traps near the medium, and introduce nematodes to take care of the larvae. Neem oil can also be sprayed for severe infestations.


Mealybugs love fruiting plants, so if you’re growing the like you’re more likely to see them. These are another ‘sucker’ type of pest, so you’ll notice weak, yellow leaves if an infestation becomes larger.

Tell-tale signs:

Mealybugs leave eggs in white, cottony looking masses on the undersides of leaves and stems (although they make be located anywhere on the plants). They leave behind a honeydew residue, much like aphids, and generally have a waxy coating.


Solutions: you can treat Mealybug problems with a gentle, natural pesticide or insecticide. You can also use a solution of 1 oz Neem oil with 1 gallon of water and spray every 1 or 2 weeks until the infestation is gone. Some helpful insects such as ladybugs can also be used.

Tip: if you catch an infestation early, you can manually destroy egg sacks with a swab soaked in alcohol and then remove them.

Spider Mites

Spider mites leave fine webs all over plants, and can be a difficult pest. They tend to infest areas with high temperatures and low humidity.

Tell-tale signs:

First, the webs. Spider mites leave behind sticky webs, just like regular spiders, but smaller and finer. Since they also suck nutrients from leaves, you may notice yellow and whitish spots on leaves. They can grow in number quickly before you notice webs, so check the undersides of leaves where they gather.  


First, manually remove areas of high infestation by pruning and removing heavily infested leaves and stems. Then you can use a safe, organic insecticide or biological insecticide to get it under control. A mixture of Neem oil and a wetting agent (for better spread) can also be sprayed every few days to kill mites and eggs.


Thrips can grow huge populations in a short amount of time, and a heavy infestation can cripple a garden if left untreated. These hyper active pests are especially attracted to light colored plants and flowers.

Tell-tale signs:

One of the biggest signs that you’ve got a thrip problem is black spots on the leaves. The black spots are actually feces dropped onto leaves. You’ll also notice that the plants they feed on get discolored spots and may appear dry.


The first thing you can do to get rid of thrips is release some insects that feed on them. Lacewings and ladybugs are typical beneficial bugs, but minute pirate bugs are most effective when it comes to thrips. If the problem grows too large, pyrethrin can be used, and followed with an insecticidal soap when needed. 


Whiteflies hide on the undersides of leaves and look like miniature moths. Like fungus gnats, they fly up in large crowds when disturbed.

Tell-tale signs:

Like aphids, whiteflies leave a sticky honeydew residue that you can spot on leaves (as well as any sooty mold that’s grown as a result). You may also see light, discolored spots where whiteflies have been feeding on leaves. Once an adult population has been established, you should be able to easily tell if they’re in your system.


To begin reducing the infestation, spray plants with water at a moderate pressure, and begin introducing beneficial insects. Like most pests, you can use ladybugs and lacewings to reduce them, as well as the whitefly parasite. Organic soap insecticides can get rid of them quickly, as can spraying with Neem oil.

I am a gardening and tech enthusiast! Stumbling across the world of Hydroponic Gardening, Aquaponics, and Aeroponics by accident I've decided to create this website to put all of the best information I can find in one easy to navigate place. I'll continue to add more content as I discover new things!

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