Hydroponic Roots Turning Brown? (7 Causes and Solutions)

Hydroponic root brown has been a headache for most hydroponic gardeners. I can vouch for this because I lost a lot of lettuce heads back then due to this plant disease! My mistake was initially ignoring symptoms such as curling and yellowing. But I’ve learned my lesson and brought them here to help you.

In general, oxygen deficiency, brown algae, slimy roots, poor water quality, hot water temperature, low pH, and inadequate sanitation cause hydroponic root brown. Root brown can be avoided with the use of air pumps, providing the best pH, water, and temperature, and practicing good sanitation.

Can you still save plants that are affected by hydroponic root brown? The first piece of advice I can give you is to keep your eyes on this page because the answer will be revealed at the end!

7 Causes of Hydroponic Root Brown (Prevention Tips)

Root brown, also known as root rot, is a disease in hydroponic plants that proliferates due to oxygen shortage, brown algae, poor hydroponic water quality, hot nutrient water temperature, and lack of sanitation.

It is not normal and is considered a huge problem for hydroponic growers. It can be difficult to spot at times because the symptoms can lead us to believe that something else is wrong.

Let us begin with the causes, and then I will list the symptoms to look out for later!

1. Oxygen Shortage

Lack of oxygen in the hydroponic water is the major cause of root brown in hydroponics. This condition is favorable to the development of Pythium spp., the fungi responsible for root brown disease. Thus, it is critical to have an abundance of bubbles in a hydroponic system.

Pro Tip: Use air pumps to increase dissolved oxygen in your nutrient water!

You might be wondering what role bubbles play in a hydroponic system.

Bubbles are ideal for every hydroponic system reservoir, especially in deep water culture (DWC) hydroponics, because they 1) increase dissolved oxygen, 2) inhibit algae reproduction, 3) regulate water temperature, and 4) displace hydroponic nutrients.

If everything appears to be in good enough condition in your system but you are still having issues, you may need a secondary air pump or a larger unit.

Caution: Root brown cannot grow in an oxygenated environment, but it is also critical to avoid excessive root disturbance. Is there such a thing as having too many bubbles in hydroponics?

   Head to our article on too many bubbles to know more about this! 

2. Brown Algae

Brown algae can also cause root rot as it blocks oxygen to enter the roots of plants in hydroponic systems. When this happens, biological processes are hindered and growth of the plant is slowed down.

Brown Algae Prevention
Brown Algae Prevention

A combination of sunlight and nutrients promotes the growth of algae. To prevent their growth, cover every possible spot so that sunlight does not reach your nutrient water.

Pro Tip: Make use of an opaque nutrient water reservoir, pipes, and tubing. Another strategy is to cover the growing medium with perlite, pebbles, or dark garments

3. Slimy Roots

Slimy roots can be caused by bacterial infection, especially in hydroponics. When slime flux dominates the roots, oxygen supply is shortened. Like the mechanism in algae, this phenomenon will cause a sluggish growth of the plant.

Pro Tip: Regulate the temperature of your hydroponic water. In deep water culture (DWC) hydroponic systems, change your water every 2-3 weeks. Another helpful strategy is to top up!

   Learn more about topping up in our article how often to change hydroponic water.   

4. Poor Hydroponic Water Quality

The use of tap water as the base for a hydroponic solution can result in mineral and salt buildup. These compounds challenge oxygen to reach the root system, resulting in rotting.

If you use tap water, several elements can accumulate in your garden soil. It is not suggested to use soft or hard water in addition to tap water. Minerals such as calcium and magnesium can be found in these water types.

 Discover more about water by reading our article on the various types of water. 

Pro Tip: Use distilled water. Distilled (or filtered) water is preferred over tap water because the distillation process removes naturally occurring contaminants such as minerals.

5. Hot Nutrient Water Temperature

The temperature of nutrient water must be kept cool because a hot hydroponic solution promotes the growth of microorganisms such as Pythium spp., the causative agent of root brown. So to maintain a normal water temperature, coat the reservoir with white paint or use reflective insulators.

Perhaps you’re wondering why white? White-colored objects reflect light. As a result, white-coated reservoirs will not capture both heat and light.

Fun Fact: Styrofoam boxes are frequently used as deep water culture hydroponic systems because they are white and act as an insulator! Thus, they are a low-cost and effective option for hydroponic gardening.

Reflective insulators, such as this one available on Amazon, are another excellent option. They reduce radiant heat gain, preventing heat absorption by your hydroponic system!

Pro Tip: Install thermometers in different spots in your growing room to monitor the temperature.

6. Low Hydroponic Solution pH

Low pH in the nutrient water favors growth of bacteria and fungi, which are causative agents of hydroponic root brown.

Pro Tip: It is best to monitor pH every 2-3 days. In general, the ideal pH for hydroponic systems is within the range of 5.5 to 6.8.

If your pH is too low, the pH of hydroponic solutions can be adjusted using commercially available pH up products like this on Amazon. But, common household items like baking soda can also be used to increase pH.

7. Lack of Sanitation

A hygienic hydroponic system, including nutrient water and gardening tools, is critical to achieving a good harvest. If the hydroponic system is not sanitized, disease transmission and root rot can occur in the following growing cycles.

One piece of advice I can give you is to clean all of your instruments regularly or between growing seasons.

Pro Tip: It is best to clean your entire system after each growing cycle. Proper sanitation will reduce the spread of plant pathogens across growing seasons.

As food growers, we must prioritize this aspect because the safety and cleanliness of our harvest are our number top priority. Remember that when growing fruits, vegetables, and herbs for human consumption, we must ensure that what we serve is safe to eat.

7 Hydroponic Root Rot Symptoms to Watch Out For

A foul smell can be observed if there is root rot. Roots may also appear slimy and brown, causing a sluggish growth. Plants may also exhibit curling leaves in an upward or downward orientation and yellowing foliage. When a plant becomes infected with root brown, it wilts, which progresses and eventually kills the plant.

Because these symptoms can be caused by a variety of factors, including lighting, pests, nutrients, and feeding cycles, they can be easily misattributed to other issues, even if they are caused by root brown.

Root rot is more common in deep water culture (DWC) hydroponics which is a system in which the roots are submerged for extended periods.

   Learn more about this hydroponic system in our article on deep water culture.  

1. Foul Smell

You can tell if there is a problem right away by raising your tank lid and smelling it. If it smells bad, you might have root brown in your system.

2. Sluggish Growth

You will know that something is wrong with your roots when they are growing slower than expected. Remember that roots are a fundamental part of your hydroponic plants because they are responsible for absorbing nutrients in the nutrient water.

Thus, another way to spot root brown is by examining the roots.

3. Browning of Roots

Some roots may become colored due to nutrients. But if they appear brown and slimy, root brown has already begun.

4. Formation of Slime Around the Roots

During the early stages of root brown, a slime will form around the roots. This barrier is strong enough to prevent any oxygen from reaching the roots, allowing infections to infiltrate, and suffocate any part of the root system.

What to Look for: A healthy hydroponic plant should have white creamy roots!

5. Curling of Leaves

Once the plants’ leaves begin to curl, it is a sign that there is dehydration happening to your plants. They curl because they are desperate to sustain the low supply of water.

When this happens, you may check the roots for brown slime which may cause the shortage of water delivered to the leaves.

6. Yellowing of Leaves

Yellowing of leaves, like curling, can occur as a result of insufficient water supply to the leaves. With insufficient water, the plant is unable to carry out its biological processes efficiently, causing its color to fade. It starts yellowing and eventually withers.

7. Plant Wilting

Wilting, as previously stated, is the end point of hydroponic root brown. If the disease spreads to the root system, it will weaken every plant part, eventually killing the plant.

3 Factors That Make Roots Strong in Hydroponics

Space in the hydroponic reservoir, oxygen access, and water temperature contribute to the overall strength and wellness of the plant’s roots.

First and foremost, let us learn more about plant roots.

The plant’s roots perform critical functions such as water and nutrient absorption, storage of produced plant materials, and physical support for the plant above ground.

Root development is a continuous process. As new roots grow, root density increases over time. Because younger root tissues absorb the majority of nutrients, new root regeneration is critical for proper plant development.

During this process, it is important to maintain the following factors for optimum plant growth.

1. Space

The roots should have enough space in the hydroponic reservoir for strong root growth and development.

To begin, your hydroponic container should be large enough to accommodate the growth of the plant roots.

Have you ever imagined being in a room that is smaller than your body? Isn’t it uncomfortable just to think about it?

The same is true for plants. You should keep in mind that the roots will quickly grow and become dense, so choose a container that is appropriate for the type of plant you’re growing. For instance, a 1 to a 3-liter container is recommended for hydroponic lettuce.

2. Oxygen

Lack of oxygen leads to suffocation. Having oxygen access fuels the biological process of cellular respiration, which is essential to developing strong roots.

The roots of plants require a lot of oxygen. To help you understand this better, did you know that plants, like humans, breathe? It is known as the process of cellular respiration in science.

Plant roots cannot respire if there is insufficient oxygen, and they will suffocate as a result. A lack of oxygen can cause root cell death and increase the risk of root diseases, such as rotting.

Pro Tip: It is recommended to use an air pump to oxygenate the nutrient water near the roots. Another tip is to not fill your hydroponic reservoir with water all the way to the top. This will provide air spaces for the roots to breathe.

3. Temperature

Hydroponic nutrient water should be kept within the range of 65-75⁰F for optimum plant growth. Too cold water temperature results in slow root growth while hot temperature breeds harmful microorganisms which can weaken the roots.

The temperature of a root zone has a significant impact on shoot growth, which includes the growth of leaves and stems. Why? Because the root is the one signaling the shoot’s growth.

Consider it similar to a football team passing the ball. The ball represents the nutrients required for growth. The root zone players will pass around the nutrients until it achieves the goal, which is to grow. The more points the root players deliver, the more the plant will grow!

Thus, you should keep a close eye on the temperature of your nutrient water.

Effect of Hot Temperature on the Roots

Bad bacteria and harmful microorganisms thrive in hot solutions. It will also be harmful to the plants’ tender roots and cause them to weaken.

Effect of Cold Temperature on the Roots

Plants, on the other hand, will grow more slowly at lower temperatures because the roots begin to shut down. Under this condition, they will not be able to get enough oxygen. As a result, the roots won’t become strong enough.

Pro Tip: The simplest way to keep your nutrient water at a comfortable temperature is to use an insulation material in your hydroponic container, such as a piece of cloth.

The question now is, how do we treat the infected roots? Is it possible to save plants once root brown has already managed to infiltrate the system?

The Best Effective Way to Treat Infected Hydroponic Roots

If the roots of the plant are severely affected by root brown, the best option is to throw away the entire plant. Trimming the infested portion of the root system will suffice if only a part of the root system is affected. Then, hydrogen peroxide must be incorporated into the flowing hydroponic water.

For Heavily-Affected Roots

Remove any whole roots that show signs of root brown and dispose of them away from your growing area. I understand how difficult it is, but believe me when I say that this is the best thing you can do to save the rest.

For Slightly-Affected Roots

Meanwhile, if root brown has not spread too far, you can simply trim the affected area and allow the roots to regrow.

Important Step: Before reintroducing the plant to the system, replace the nutrient water and add a small amount of food-grade hydrogen peroxide.

Hydrogen peroxide is a good disinfectant that fights root brown while having no negative effects on your plants.

You can also use root builders to help your roots grow stronger. These contain a high concentration of beneficial bacteria and aid in the aeration of your nutrition solution.

   To know more about disinfectants, go to our article on hydrogen peroxide vs bleach. 

How to Achieve Strong Roots in Hydroponics

Strong hydroponic roots can be achieved by avoiding root wounds when transplanting, not submerging the roots fully in water, and covering any possible entry point of sunlight to the water reservoir.

Wounding and Hydroponic Roots
Wounding and Hydroponic Roots

During transplanting, seedling roots should not be overly disturbed. Roots at that stage are extremely delicate and require special care, so be cautious when transplanting. Wounds on your roots can serve as entry points for bacteria and fungi.

Next, do not completely immerse the roots in the nutrient solution. As previously discussed, oxygen is critical, so having an air space in the roots will result in the growth of healthy roots.

Caution: Another possible problem that may harm your roots is algae growth. It is aided when sunlight enters the hydroponic reservoir. Since the water is enriched with nutrients, algae will feed on these nutrients that are present in the solution.

Solution: To keep your roots well and strong after transplanting, cover any transparent surfaces to prevent sunlight from reaching your nutrient water.

Hydroponic root rot: prevention, detection, elimination (2020)


Is hydroponic root brown contagious?

Yes, root brown is contagious. Considering the fact that it is caused by an organism that can be transferred through water, root brown can spread easily, especially in circulating systems such as nutrient film technique (NFT) hydroponics.

Is fungi the only microorganism that causes hydroponic root brown?

Other than fungi, oomycetes are another group of pathogens that can cause hydroponic root brown. They have growth mechanisms that are similar to fungi but differ in evolution. Phytophthora spp. belong to this group and infest peppers and tomatoes.

Summary of Hydroponic Root Brown

Lack of oxygen, brown algae, slimy roots, poor water quality, hot water temperature, low pH, and insanitation are causes of hydroponic root brown. Wilting and curling leaves are common symptoms of hydroponic root brown. To have strong roots, space, oxygen, and proper temperature must be provided.

To prevent root brown, one can install an air pump to increase bubbles in the hydroponic solution. Providing a cool growing location with temperatures ranging from 65 to 75° F is also optimal for the plant’s growth. Lastly, cleanliness must always be observed in the garden tools and in the hydroponic systems to hinder the spread of the disease.

If the plant’s roots are highly affected by root brown, the best option is to discard the whole plant. However, when only a small portion of the root system is affected, trimming the infested part will do. Afterward, hydrogen peroxide must be added to the circulating hydroponic water for continuous disinfection.


  • “Brown Root Rot” by Brooks, F.E. in The American Phytopathological Society
  • “First Report of Root Rot of Hydroponically Grown Lettuce Caused by Pythium myriotylum in a Commercial Production Facility” by Stanghellini ME, Kim DH, Rakocy J, Gloger K, Klinton H. in Plant Diseases
  • “How to Sanitize and Sterilize Hydroponic Systems” by Godfrey, M. in Upstart University
  • “Understanding Root Rot Disease in Agricultural Crops” by Williamson-Benavides, B.A. and Dhingra, A. in Horticulturae 2021

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