Root rot detection, treatment, and prevention

Did you know that more houseplants die from overwatering than from lack of water? That is due in no small part to root rot, which is encouraged by waterlogging.

How you can recognize, treat and prevent root rot is explained here! I do not use the usual methods, where you can only hope and show you what actually works. 

Many dark brown to black roots are rotting on a plant. Root rot has already affected much of the root ball. Only a few bright, healthy roots remain.
(Image: © NokHoOkNoi –

What is root rot?

Before we get into what you can do about root rot, let’s briefly clarify what root rot even is. As the name implies, root rot is when a plant’s roots rot.

More precisely, the epidermis of the root dies first. Since this absorbs water and nutrients, the root can no longer survive without it. Then the now-exposed layers under the epidermis are attacked.

That leads to the gradual death of more and more roots. The root rot eats its way through the root system. It can also happen that the trunk and the base also start to rot. That is called stem rot or base rot.

Root rot also causes the health of the plant to decline quite quickly. Thus, the houseplant may shed leaves, or entire shoots may die.

In addition, root rot is not picky. Any plant can be affected. However, in some plants, the rot occurs more often than in others. 

Causes of root rot

The causes of root rot can be highly complex and challenging to pinpoint. But they don’t have to be. In many cases, root rot is caused by care errors.

It is essential to know that the bacteria and fungi that can cause root rot are already present in the substrate. That is not a problem at first, as the plant’s defenses can withstand them in a healthy state without any issues.

It becomes problematic when this balance falters. That allows fungi and bacteria to multiply optimally in wet and permanently moist substrates.

Root rot due to care errors

In most cases, the foundation for root rot is laid by too much moisture, often caused by overwatering. In this case, the roots suffocate, and after that, they begin to rot or decay. 

That is favored if your plant is in the wrong substrate for houseplants.

Another reason can be insufficient watering. In this case, the roots dry out and die as a result. If they are now moistened again, they provide a good breeding ground for various bacteria and fungi.

Root rot caused by bacteria

Infection with bacteria often occurs shortly after or in parallel with a fungal infection. It is recognizable by brown, sometimes muddy spots that smell of decay. These do not necessarily have to be near the roots but can occur throughout the plant.

Unfortunately, no home remedies or other aids will help with root rot caused by bacteria. In many cases, therefore, the plant must be disposed of.

Bacteria that can trigger root rot include:

Root rot caused by bacteria

If the roots are not dying due to maintenance errors, fungi are the next suspect. Several fungi can attack the plant and its root system. The two most common are Phytophthora and Pythium.

Their spores linger in the substrate for a remarkably long time. That is one of the reasons why you should not reuse old substrates.

These fungal spores can also be transferred to other plants. That happens either through the air or insects. For example, fungus gnats living in and on the substrate can transfer these spores to other plants.

Theoretically, a plant affected by root rot and fungus gnats at the same time is likely to infect other plants. Practically, however, this only works if the other plants provide a suitable breeding ground – in our case, too much moisture.

Healthy (left) and diseased root (right) in direct comparison
Root rot eats into the root. That can be seen on the right side of the picture. Short the root to a point without root rot towards the plant. As seen on the left side, a healthy root has a bright, vital color and no dark, rotting areas.

Detecting root rot

Root rot often remains undetected for a long time. Only when it has progressed can it be recognized on the visible part of the houseplant. There are many different signs.

I have listed a selection of them in descending order of frequency.


Waterlogging is root rot’s most common cause and the most apparent identifier. If water stands in the saucer for a long time or the substrate is swellingly wet, root rot is almost certainly the result.

An unpleasant odor and yellow leaves often accompany it.

Discolored, yellow leaves and black leaf spots

If the lower leaves turn yellow, this can also indicate rot. After that, they usually start to turn brown from the outside. Especially if the substrate is wet simultaneously, you should examine the roots.

Another sign can be black spots on the leaves.

Withered shoots

After the leaves, the shoots also start to wilt. If this does not change when you water the houseplant, you should also check the roots. You should be especially alert if the shoots appear suddenly and without any change in care.

Discolored and rotting roots

Healthy roots of most plants are whitish to reddish. If they take on a brown color and become soft, it is root rot. If unsure if a root is rotting, you can roll it gently between two fingers.

If it is soft, mushy, or coming off the plant, it is rotting.

Soft stems and bases

If root rot is advanced, it can also affect the base of plants. In this case, they become soft. Therefore, if you suspect it, gently press the base and shoot. If it feels soft, it may be already advanced root rot.

Plant stands shakily

Even more evident than the previous point is the extent of root rot when the plant loses its support. In this case, not enough healthy roots are left to stabilize the plant. Again, I strongly recommend taking a look at the roots.

Foul smell

If the root rot has been present for some time, a foul odor will spread around the plant. It is a pretty clear indicator and should be investigated.

Slow growth

The last and probably the most inconspicuous indicator is slow growth. That can have various reasons, such as location and nutrient supply. However, if your houseplant is in a suitable place and is sufficiently supplied with nutrients, it may be worthwhile to look at the root system.

What do roots affected by root rot look like?

Healthy roots generally have a lighter shade. That varies depending on how your plant is kept. If you keep it in passive hydroponics, the roots are almost white to beige.

In substrate, they are slightly darker. Here they are a light to medium shade of brown. Coco soil can make them a little darker in color. However, there are also plants with pink to red roots.

If the roots are affected by rot, they will be dark brown to black. They smell rotten and feel soft to the touch. Often you can easily strip off the tissue around the core of the roots.

Decomposing, rotting roots can be seen next to healthy, light-colored roots.
Rotten roots can be identified by their black and unhealthy appearance. Healthy roots are light-colored, retain their shape, and are often hairy.

Treat root rot

Now we come to the exciting part. We assume you’ve already taken your plant out of its pot and identified root rot.

The next step is to remove as much substrate as possible. Not only will this make it easier for us to examine the roots, but it will also simultaneously counteract the return of fungal root rot.

Fungal spores and dead roots can encourage healthy roots to rot. Therefore, discard the old substrate. If you use a mineral substrate such as expanded clay, you can boil it and reuse it.

Now that the soil is removed, I recommend rinsing the roots once to remove the last substrate residue.

Once this is done, the next step is to get a clean and sharp blade. Disinfect it before and after the treatment. This way, you prevent the transfer to other plants and healthy roots.

Now examine the root system for rotting roots. If the root is not completely rotten, cut it off about 1 inch above the rotting part. This way, you have a buffer in case the rot is not visibly already more advanced.

Do not cut the root entirely if it is not rotting to the base.

If you are unsure whether a root is rotting, you can gently twist it between your fingers or pull on it. If it comes off the plant without any problems, it is deteriorating.

Now we come to probably the most crucial step – disinfecting. Prepare a mixture of No products found. and water for this. I use a ratio of 1:1, so one part water and the same part hydrogen peroxide.

If you are unsure (I was the first time), you can use a ratio of 2 parts water and 1 part hydrogen peroxide.

Dip the root system into the solution briefly. A longer soak is not necessary. The hydrogen peroxide will reliably kill bacteria and fungi.

If you don’t have hydrogen peroxide at hand, you can also use No products found.. Here you can add 3 to 6 drops to 0.26 (1 liter) of water. Another remedy I could not test myself yet is a solution of 1 tsp neem oil*, ½ tsp liquid soap, and 0.26 (1 liter) of water. 

After that, you can optionally use a No products found.

The next step is to replant the plant. However, please do not use the old substrate as it is contaminated. So the root rot would almost certainly return. You can also sterilize or dispose mineral substrates such as expanded clay pebbles.

If you want to use the old pot, I recommend cleaning it thoroughly and with an aggressive cleaner beforehand.

If your houseplant has lost a lot of roots, you should choose a smaller pot. This way, you will reduce the chance of overwatering. In these cases, I have had a good experience with Sphagnum moss instead of a substrate. Just keep it moist and not wet.

Do not use fertilizer for the next 10 to 12 weeks. Although you might think that nutrients are just the thing to bring the plant back to old health, not using those nutrients sets stimuli for root retention.

The plant thus tries to reach the missing nutrients through more roots.

Last comes probably the most emotionally difficult step for you: Removing leaves. But why would you remove leaves when the roots are already a construction site for the houseplant?

Leaves are crucial for photosynthesis, but they also evaporate moisture. That is not a problem if the root system is adequate, as new water constantly circulates through the plant. However, the plant cannot adequately supply the leaves without this root system.

Therefore, you should remove leaves in proportion to the roots lost. So if your plant has lost half of its roots, I recommend you remove half of the leaves.

Alternatively, now is your chance to cut a cutting instead of the leaves. That way, you have a backup in case your plant has lost too many roots or doesn’t survive for other reasons.

Try to keep the plant relatively dry in the coming weeks. So water only when the substrate has dried out superficially. This way, you avoid creating optimal conditions for fungi and bacteria.

A gentle pull can quickly identify roots affected by root rot.

Prevent root rot

So now it’s done. Your plant has been treated for root rot and is on the road to recovery. But how can you prevent root rot from occurring again?

Prevent waterlogging at all costs

Waterlogging not only suffocates the roots but also provides sufficient moisture to create optimal habitats for bacteria and fungi. Therefore, you should only water your plant when necessary and avoid a fixed watering routine.

Do not use organic substrate more than once

Old substrate should not be reused. Generally speaking, nutrients decrease over time, and properties can also change. If a plant had root rot in the substrate, it is contaminated.

If it is reused, the plant will almost certainly get root rot again.


Overfertilization can also lead to root rot, as the roots burn and die. So the fungi and bacteria have a good breeding ground here too.

Root rot caused by overfertilization tends to develop into stem rot quite quickly.

Use cinnamon

Cinnamon can not only help against pests but also give fungi. It can also stimulate the plant to grow new roots. You can either add cinnamon* to the substrate or mix it in. 

Alternatively, you can make a spray:

  • Put 0.26 (1 liter) of water in a bowl
  • Mix 2 tablespoons of cinnamon in the water
  • Let the mixture sit overnight
  • Filter the mixture (e.g., with a coffee filter)
  • Pour the filtered cinnamon water into a clean spray bottle

If needed, spray it on the substrate or directly on the roots. Use natural cinnamon and not a cinnamon blend for either method.

Use hydrogen peroxide from time to time

Hydrogen peroxide can be used not only when root rot is present but also as a preventative measure. So now and then, you can water your plant with a solution of one part No products found. and one part water.

That helps against fungus gnats and keeps the bacteria and fungal spores in check. But don’t forget that good bacteria and beneficial insects like springtails will also suffer under this treatment.

Another benefit of hydrogen peroxide is that it brings oxygen to the roots.

When watering, don’t be irritated by the enthusiasm of the substrate. That is the usual chemical reaction.

Keep an eye on oxygen levels and pH in mineral substrates

If root rot occurs while using a mineral substrate, there is often too little oxygen in the water, or the pH is too low.

Change the water in your hydroponics regularly or add oxygen to it. Depending on the plant, the pH should be between 5.0 and 6.5.

A long, dark-colored root can be seen, which has been attacked by root rot.
Remove roots affected by root rot completely. After removing the roots, I recommend treating the root system with a 3% hydrogen peroxide-water solution.

My conclusion

In case of root rot, haste is necessary. The more roots are affected, the lower the chance of survival. Therefore, it may be better to take cuttings and root them in some cases.

However, many plants can recover and grow to their former glory with the proper measures. For example, one of my Monstera adansonii variegata lost virtually all of its roots.

After about three months, it returns to where it was before root rot. So don’t give up hope!

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About the author
Richard Schmidt
Hey, my name is Richard! In my spare time, I write about the care of indoor plants on this website. Indoor plants have long fascinated me. That's why there are many plants in my little urban jungle - from the mainstream Syngonium to true rarities. Besides my passion for houseplants, I'm a real sneakerhead.

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