Root Rot in Hydroponic Systems (How to Fix it Fast!)

Yellow plants, stinking roots, and dead crops – is there anything more heartbreaking than root rot in a home hydroponic system? Even commercial hydroponic growers fear an outbreak of root rot in hydroponics systems. 

For the home grower, it can spell the end of a whole season’s worth of crops. 

Prevention is always better than cure, so let’s look at how to prevent root rot in hydroponic systems and what you can do if disaster strikes.

What is Root Rot?

root rot hydroponic system progression

Root rot occurs when pathogens attack the root system of a plant. They devour the plant’s roots, breaking down cell walls and killing off the tissue. The dead roots then disintegrate and shed dead plant material through your system. 

Without roots, the upper portion of the affected plant starts to flag. It can’t get enough water or nutrients. The leaves soon die, and the rot moves upwards into stems and stalks. From there, the entire plant rots from the root up.

Even well-maintained hydroponics systems and somewhat aquaponics systems are the perfect breeding ground for these nasties. In circulating systems like Nutrient Film Technique or Ebb and Flow, the nutrient solution itself becomes the key vector. 

Healthy and unhealthy roots alike are washed with the same water solution, making it very easy for one sick plant to infect every healthy plant in the rig quickly. 

Deep Water Culture systems are even more vulnerable, with the entire system resting over the same infected reservoir water.

What Causes Root Rot in Hydroponic Plants?

While poor conditions can contribute, the main cause of root rot is a disease-causing invader. 

Root-related plant diseases are driven by a suite of harmful microbes.

Most of these occur naturally in most garden soil, where other beneficial microbes keep them in check. They thrive in warm temperatures and low oxygen levels that sometimes develop in even a well-maintained hydroponic setup. 

Without the growth of bacteria hostile to them, these pathogens can quickly wipe out your entire hydroponic garden.


A Pythium infection is a substantial problem across all hydroponic cultivation. This family of microbes is a form of water mold called an oomycete. It remains dormant if there’s no plant to attack and spreads as airborne spores and infected water. 


Phytophthora is another water mold with a strain that attacks just about every crop. Like Pythium, it remains dormant in the soil for years and can survive on hard surfaces and equipment.


Fusarium is caused by the fungus Fusarium oxysporum. It causes not only root rot but crown and stem rot as well.


Rhizoctonia is caused by the fungus Rhizoctonia solani. It causes reddish-brown lesions in the stems and stalks in addition to black or brown roots.

Black Rot

Black Rot is caused by Thielaviopsis basicola. It loves alkaline conditions and can develop if your pH creeps above 6.0.

How to Identify Root Rot Symptoms in Hydroponics

roots of hydroponic vegetables

To identify root rot, thoroughly examine the roots of the plant. Many early signs of root rot are similar to those of nutrient deficiency or dehydration from an overly-rich nutrient solution. Inspection of plant roots is needed to confirm a case of root rot.

Healthy roots are pale in color. They should be white or cream, with many fine secondary roots visible on the surface. These fine roots generally don’t form clumps or twisted mats but will flow freely when immersed in clean water. 

Healthy roots are also largely without odor, at most smelling of the plant in question. Mint roots may have a minty freshness when disturbed, for example.

Diseased roots, on the other hand, will be red, dark brown, or black. Sick roots are slimy and often disintegrate when handled. They’ll also stink to high heaven, reeking of rotten eggs or fish.

Signs in the rest of the plant include dead leaves or leaves that turn yellow from the tip down. The plant wilts and stops growing. In some cases, they will rot from the top down, too. Stems and stalks closest to the growing medium may change color and become soft or develop open sores. 

Keep an eye out for fungus gnats. Not only can they spread the pathogens that cause root rot, but they are drawn to decay. Their presence indicates problems with your growing medium. 

Treating Hydroponic Root Rot

rotting roots in hydroponic system

Much of what you can do to treat root rot will depend on how early you’ve caught it, what you are growing, and what kind of rig you have.

Circulating systems can sometimes be saved at the early stage by changing the hydroponics water and flushing the plants’ roots with a solution of 35% food-grade hydrogen peroxide (H2O2). 

It must be diluted first at a rate of one part (H2O2) per 11 parts distilled water. This will give a 3% solution that is ideal for sterilizing equipment. Use it on the grow bed, any trays or gutters, and through the plumbing. It should be mixed fresh each time you use it.

You can use this solution to sterilize living roots. Add about 3ml per quart directly to your nutrient solution every four days. It breaks down over time into water and oxygen, leaving no dangerous residue behind. Once the root mass is clear of signs of rot, you can return to a standard nutrient solution.

Passive systems must be emptied, and the hydroponic reservoir must be scrubbed thoroughly before you can treat them with this approach. It’s riskier, and you may well lose your crop regardless.

Dilution Table for Hydrogen Peroxide (H2O2)
For sterilization3%1 part 35% H2O2 with 11 parts distilled water
To supplement nutrient solution0.1% approx.3ml 3% solution per liter or quart.

Treating root rot with hydrogen peroxide is a temporary solution. It can get your crops to the point of harvest, at which point you should strip the system, sterilize thoroughly and start again. 

Infected crops grown in bedded systems like ebb and flow, Dutch buckets, and wicking beds are usually doomed. 

The growing medium will be compromised and impossible to sterilize. It’s one of the reasons commercial growers work so hard to control root pathogens. An infection can wipe out a whole season’s crop, even with the most cutting-edge solutions available.

Root Rot Hydroponic Pro Tip

35% food-grade hydrogen peroxide concentrate is very powerful. It’s caustic and can cause damage to the skin, eyes, and other delicate plant tissue. Always wear gloves and eye protection when handling it, and never use it undiluted for any purpose. 

Some crops are more difficult to save than others. Lettuces and leafy greens will struggle to survive even after you treat them, and in more cases than not, they will die regardless. They have a short life cycle and just don’t have the time or resources to spring back even once their roots recover. 

On the other hand, perennials like tomatoes, peppers, and the like will often respond well to treatment. They may fruit less abundantly, but you’ll still get some return for the effort. 

If you decide your best way forward is to purge your infected plants, thoroughly sterilize the entire rig afterward to prevent fungal disease in future crops.

Preventing Root Rot in Hydroponic Systems

healthy hydroponic plant roots

The following methods can be applied for the best chance of preventing root rot in your hydroponics system.

Add Oxygen to the Root Zone

One of the best preventative measures is to keep your hydroponic nutrient solution full of enough oxygen. Most unwanted pathogens struggle in an oxygen-rich environment.

Air pumps and air stones are a good solution for passive systems like Deep Water Culture rigs. They’re cheap to buy and run and can be popped straight into the reservoir with very little fuss. 

An air pump is more suitable for larger systems.

Provide Good Drainage

Almost all root pathogens need wet conditions to thrive. They may linger in the soil, lying dormant until the root system is subjected to poor drainage and stagnant water.

Circulating systems need a medium that allows good flow through, like LECA or perlite. Mediums like LECA are perfect for hydroponic trees, which need plenty of air circulation in the roots when starting out. Don’t overdo it with absorbent mediums like peat moss or coir or other similar organic matter; this will hold more moisture than required.

Passive systems can present challenges for drainage. Wicking beds need the right blend for the plant in question and make sure to use an appropriate number of wicks for your bed. 

In most Deep Water Culture systems, ensure the water level allows some clearance at the base of the plant. There needs to be a small gap to allow oxygen to the roots. It’s not true ‘drainage,’ but it serves the same purpose.

Change your Hydroponic Solution Regularly

Hydroponic nutrient solution has a finite lifespan in your rig. Nutrient imbalance can weaken the roots and make the plants more vulnerable to attack. It also plays host to the oocytes and spores that spread disease.

Depending on your rig, it’s best to change the entire solution no less frequently than once every three weeks. In hot weather, you’ll need to do it more often to allow your mature and young plants to remain hydrated and at the right EC.

Maintain Correct pH Levels

Dangerous fungi and bad bacteria prefer neutral to alkaline conditions. Thankfully, this is generally the opposite of what plants growing in hydroponics require. If you can keep your solution mildly acidic, you will prevent many of the most virulent pathogens from setting up camp. 

Lower pH will also prevent nutrient deficiencies and allow the best growth from your plants.

Maintain a Cool Water Temperature

Much like acidity, cool water can prevent root rot. High temperatures at the root zone reduce the amount of oxygen the water can hold and promotes the growth of unwanted pathogens. Keep the water temperature at the lower end of what your crops will tolerate. 

Some, like brassicas, can be grown at temperatures low enough that even the big baddies like Pythium don’t stand a chance.

Ensuring your reservoir is dark helps keep things chill. Too much light inside the tank can heat the water, especially if the room temperature is already higher than ideal. Insulation is a good idea too.

Maintain Good Hygiene in Your Growing Space

Wherever possible, treat your grow area like a sterile environment. Always wash your hands before and after working with your plants – it’s one of the easiest ways to prevent the spread of bacteria. Sterilize tools before use with rubbing alcohol, and never bring tools used for outdoor gardening anywhere near your hydro setup. 

Make sure dead plant matter from sick plants is disposed of in household garbage promptly.

Add Beneficial Bacteria

The roots of plants in conventional agriculture are awash with good bacteria that keep disease at bay. Hydroponic roots don’t get the chance to develop the beneficial root bacteria that helps protect them from root problems. 

You can help the roots of your plants by investing in one of the many commercial probiotic formulas that include these helpful little microbes. Consider it a bit like having a dose of kombucha or live culture yogurt. This is one of the best methods to set the stage for good root health.

Frequently Asked Questions About Hydroponic Root Rot

hydroponic plants in LECA

Why Are My Hydroponic Roots Brown?

Infected roots often change color. As they decay, they turn brown or black. Some diseases, like Rhizoctonia, can cause red or orange roots too. If your plants are thriving and have otherwise healthy-looking roots, the brown color may be from the nutrient solution itself. 

Some brands use minerals that stain. If you have tide lines or brown marks in your reservoir and plenty of new roots, it’s likely your solution is to blame.

Can Plants Recover From Root Rot in Hydroponics?

While it’s possible for plants in hydroponics to recover from root rot, it’s simply not worth the effort for many. Short-cycle crops like lettuces won’t have the time to regrow rotten roots before you pop them out to eat. 

Many treatments, especially commercial fungicides and the like, leave buildup on and inside the leaves that can be hazardous. If a case of root rot does appear on your plants, using all-natural fungicides like neem oil or neem oil mixtures are your best option.

Larger, longer-lived plants will recover in time if you treat them. If you have a special chili or a beloved heirloom tomato vine, it’s worth trying to save them.

Can I Transplant My Plants with Root Rot from Hydroponics to Soil?

Yes, although you should be sure to cut away any diseased roots before transplanting hydroponic plants into soil. The harmful bacteria could spread through your garden or soil if introduced into the environment.

Does Root Rot Spread in Hydroponics?

Hydroponics is almost tailor-made to support the spread of root rot through the whole system. Systems that collect and reuse the nutrient solution will also circulate the pathogens that cause root rot in hydroponics. 

Plants in deep water systems have roots in close proximity. Even relatively contained systems like Dutch bucket drip setups often have the plants tightly packed in ways that promote the spread of disease.

It’s critical that you do everything you can to prevent diseases from making their way into your grow room or greenhouse in the first place. Good hygiene costs very little and should be the first step to saving you a world of hurt down the track.

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