Root rot in hydroponics is a huge concern due to the amount of water that hydroponic roots are exposed to. Root rot issues are caused by bacteria, mold, or fungus. Root rot will cause your hydroponic plants to drown. The main way to prevent root rot is to keep a clean and well-maintained hydroponic system.

Read on to learn about hydroponic root rot!

What Is Root Rot and What Causes It?

Hydroponic root rot happens when your growing medium is too damp because of poor drainage or overwatering. It’s caused by bacteria, mold, or fungus.

It starts to grow on your plants’ root systems when they’re too moist. When this happens, the roots don’t get enough oxygen and begin to decay.

Rhizoctonia, Pythium, Phytophthora, and Fosarium fungi are the most common culprits of root rot.

One of the worst things about root rot is that it can be transferred among plants. So if one of your plants gets root rot, all of your other plants become at risk.

To prevent root rot you need to be sure that your growing mediums are properly aerated, have good drainage, and are sterile.

How To Tell If Your Hydroponic Plant Has Root Rot

If your hydroponic plant has root rot, the formerly-healthy roots will start to turn yellow and then eventually turn brown. The roots become tangled, slimy, and may start to smell.

The plant itself may also begin to wilt and become discolored as it can no longer take up nutrients.

Healthy hydroponic roots are white or have a creamy color. Root decay will cause root discoloration such as black roots.

Can Root Rot Happen In Any Hydroponic System?

Root rot can happen in any hydroponic system. However, it’s most likely to occur in deep water culture, ebb and flow, and hybrid systems.

Hydroponic systems that keep the roots submerged in water for extended periods are the most prone to root rot.

In addition, if a system malfunctions or isn’t properly maintained it is also prone to root rot.

Aeroponic systems are the least likely to develop root rot due to the amount of aeration that the roots get.

What Does Root Rot Smell Like?

Smell is one of the first signs of root rot that you may notice. Root rot in hydroponics smells quite potent and swamp-like. Think rotten eggs.

Other root rot may smell like the plants you have growing, just a little stronger. This is typically the beginning sign of hydroponic root rot.

But once your plants are starting to die, the smell will become quite unpleasant.

How To Prevent Hydroponic Root Rot

treating hydroponic root rot

Here are some of the best ways to prevent hydroponic root rot:

  • Keep the temperature of your system regulated, both above the roots and in the water.
  • Oxygenate the roots of your plants so they don’t suffer from a lack of oxygen. Consider air stones.
  • Keep up with maintenance so that your hydroponic system is sterile and clean.
  • Properly cover your root systems to protect them from excess light.
  • Add beneficial bacteria to the hydroponic water reservoir. The protective bacteria will fight off pathogenic bacteria and keep away all those nasty pathogens.
  • Prune your root beds so they don’t clog up your system. This is also important for root health.
  • Pay close attention to every single individual plant since root rot can spread.
  • Avoid poor water circulation.
  • Maintaining the correct pH levels.

Can A Plant Recover From Root Rot?

Plants with root rot can recover from it as long as the infected plants are found and treated in a timely manner.

If you notice wilting leaves and a strong smell, investigate right away. This is especially important if the wilting seems to be sudden.

If the plants with infected roots have more dead or wilted leaves than green leaves, it may be beyond the point of no return.

In addition, some plants such as leafy greens aren’t quite worth saving once root rot kicks in. But plants like tomatoes, peppers, and basil are worth your time to save since the root rot doesn’t bother the edible parts of the plants and regrowth is quick.

Best Ways To Treat Root Rot

Here are some of the best ways to treat plants with root rot and prevent future root rot in hydroponics:

  • Water and hydrogen peroxide
  • Cutting off damaged parts of the plant and dead leaves/brown leaves.
  • Adding beneficial bacteria
  • Spraying apple cider vinegar and water on your plants
  • Combining all the above methods

A little bit more about hydrogen peroxide:

Hydrogen peroxide is well known for its ability to kill root rot. It’s quick, effective, and affordable.

First, carefully remove the rotting or damaged parts of your plant besides the roots.

Now empty all the water from your hydroponic system. Scrub it down extremely well and rinse it many times.

Refill your reservoir with fresh water and make sure it’s the right temperature. Add 3 mL of hydrogen peroxide per each gallon of water.

After one day passes, go through the process once or twice more.


Many hydroponic growers run into issues with root rot. Although root rot in hydroponics is a grave concern, there are mitigation methods to avoid and treat it. Thankfully, it won’t kill all of your plants as long as you’re paying attention. Use the tricks discussed in this article and you’ll be safe from root rot!

Check out the rest of our blog for more hydroponics tips and tricks!