Why Are My Hydroponic Roots Brown? (The Battle Against Root Rot)

If you’re a hydroponics enthusiast, you’re aware that this soilless cultivation method brings a unique set of challenges. One such challenge that you usually don’t encounter when gardening in soil, is a sudden browning of the roots. Hydroponic roots that turn brown, slimy and emit a strong odor are likely being affected by root rot, decay and the proliferation of fungus due to lack of oxygen in the root zone. This article aims to demystify the root rot phenomenon, exploring its causes, symptoms, and solutions, and how to prevent it.

Roots beginning to decay

Understanding Brown Roots in Hydroponics

In a hydroponic system, plants grow in a nutrient-rich solution rather than soil. The roots, supported by inert mediums like clay pellets, perlite or peat moss, are submerged in this solution. Healthy roots have a creamy color and firm texture. So, when roots turn brown or black, it’s generally a warning sign of root rot.

What is Root Rot?

Root rot is a condition that affects both conventional and hydroponic plants. It’s a water-borne disease that causes roots to decay and eventually die due to oversaturation and insufficient drainage. In the case of hydroponic plants, the continuous exposure to water can inhibit the aeration of oxygen, leading to root rot.

The Pathogens Behind Root Rot

Hydroponic systems can be breeding grounds for various pathogens, including water-borne fungi like Phytophthora, which is a potent plant pathogen. Other common root rot pathogens include Pythium, Rhizoctonia, and Fusarium. These pathogens can drastically limit the plant’s ability to absorb nutrients, leading to plant death.

Identifying Root Rot in Hydroponics

Identifying root rot early is crucial to save your hydroponic plants. Here are key signs of root rot:

  1. Root Discoloration: Healthy roots are a creamy color. Discoloration, from yellow to brown and eventually black, is a common sign of root rot. However, remember that some nutrient solutions may stain roots, causing harmless discoloration.
  2. Earthy Odor: If you detect an earthy smell, it may be a sign of root rot. Hydroponic systems shouldn’t emit any earthy odors as no soil is involved.
  3. Slimy Roots: Pathogens can create a slimy barrier around roots, preventing oxygen absorption. If the roots of your plants are slimy and mushy, it’s likely due to root rot.
Decomposed plant roots and algae slime

Can You Save a Plant With Root Rot?

If root rot has advanced to the stage where roots are brown and mushy, it’s unlikely the plant can be saved. The best course of action is to remove the plant and rectify the issues causing root rot. However, if caught early, root rot can be treated, and the plant saved.

Treating Root Rot: A Step-by-Step Guide

  1. Shut Down the System: Turn off your hydroponic system and carefully remove the affected plant.
  2. Rinse the Roots: Run the roots under clean water to get rid of dead roots and debris.
  3. Prune Infected Roots: Using sterilized scissors, cut back any roots affected by rot.
  4. Sterilize the Roots: Soak the root system in a sterilizing solution for about 12 hours.
  5. Clean the Reservoir: Drain and clean the hydroponic reservoir, ensuring all traces of the old nutrient solution are removed.
  6. Restart the System: Reassemble your hydroponic system and add fresh nutrient solution.

IIs your rockwool turning green? Check out this article to find out why.

Using Beneficial Bacteria

Once your system is up and running again, consider introducing beneficial bacteria. These good microbes can help fight off harmful fungi, protect roots, and enhance root mass and vigor. One recommended option is Hydroguard, which can be added to the reservoir at a rate of 2 ml/gallon every cycle.

How to Prevent Root Rot

Prevention is better than cure, especially in the case of root rot. Here are some ways to ensure healthy root growth and prevent root rot:

1. Maintain Proper Aeration

Proper oxygenation is key to preventing root rot. Using an air pump to add more bubbles can improve oxygenation, making it harder for root rot pathogens to establish themselves.

2. Keep Roots Dark

Roots prefer darkness. Excessive light can trigger the growth of harmful organisms. Use a thick, opaque vessel for your water reservoir and dark tubing for your system to prevent light from reaching the roots.

3. Control Temperatures

Keeping your hydroponic setup cool helps prevent root rot. Aim for a temperature range of 65-85°F in your water reservoir. Regularly monitor water temperatures and consider using exhaust fans to maintain optimal conditions.

4. Avoid Water Changes

The water in your hydroponic reservoir forms a unique ecosystem, balancing itself over time. Changing the water can disrupt this balance and stress the plants. It’s better to keep the old water and top it off with additional nutrient solution as needed.

5. Clean and Sterilize Equipment

Regularly cleaning and sterilizing your hydroponic equipment helps prevent the spread of pathogens. This includes not just the reservoir and tubing, but also scissors, hoses, and other tools.

Adding fresh oxygen and water to a reservoir


Brown roots in hydroponic plants are usually a sign of root rot, a serious condition that can kill your plants if not addressed promptly. Early detection and action are crucial. By maintaining proper aeration, keeping roots dark, controlling temperatures, avoiding water changes, and regularly cleaning and sterilizing equipment, you can prevent root rot and ensure healthy growth in your hydroponic garden.


Located in Portland, Oregon, Tim started gardening in his 20's and after a couple of decades felt like he had some things to share.

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