How to identify and fix cannabis root rot

Adam Parsons

Cannabis Journalist & Staff Writer at Zamnesia

Adam Parsons

Last updated: January 31, 2022

Spotted drooping plants or slimy roots? Don't panic! Here's how to tell if it's root rot and what to do about it. Regardless of your growing setup, cannabis root rot can quickly derail all of your hard work and eventual harvest if left unchecked.

In this guide, we'll help you understand what root rot in cannabis is, how to identify root rot symptoms early, especially in the leaves, how to fix root rot in soil and hydro setups, and how to prevent it from striking again. From recognizing discolored, mushy roots to restoring oxygen in your system, we'll take you through every step to keep your cannabis plants healthy, vibrant, and rot-free.

What is cannabis root rot?

Cannabis root rot is a common yet potentially devastating condition that affects the root systems of cannabis plants, particularly in hydroponic setups and poorly managed soil grows. It occurs when roots are deprived of oxygen and become vulnerable to harmful pathogens, most commonly Pythium, a water-borne microorganism that thrives in wet, poorly aerated environments.

Healthy cannabis roots should be firm, white, and odorless. In contrast, roots affected by rot become slimy, discolored (brown or grey), and emit a foul, swampy smell. If not addressed quickly, root rot can disrupt nutrient uptake, damage the plant's vascular system, and eventually kill the plant. Understanding cannabis root rot is the first step to stopping it in its tracks.

What causes root rot?

Several factors contribute to the development of root rot in cannabis plants. The condition usually stems from a combination of poor environmental control, pathogen exposure, and oxygen deprivation. Here are some of the typical causes of root rot:

• Pythium and other pathogens: Pythium is one of the most common culprits behind root rot cannabis issues. This parasitic oomycete attacks weakened roots, rapidly spreading decay and compromising plant health.
• Poor drainage and overwatering: In soil-based grow-ops, root rot often results from waterlogged substrates and compacted soil that restricts airflow. Overwatering saturates the root zone, making it a breeding ground for harmful microbes.
• Lack of oxygen in hydroponic systems: In hydroponics, stagnant or unoxygenated water allows pathogens to flourish. Without adequate aeration (air stones or pumps, for example), roots suffocate, and decay sets in fast.

While symptoms of cannabis root rot may appear similar in both soil and hydro setups, the cause often differs:

• Hydroponic systems: These are particularly susceptible due to the reliance on water as the primary medium. If the reservoir lacks movement or proper sterilization, pathogens can quickly take over. Sudden outbreaks are common and often severe.
• Soil grows: Though less common, root rot in soil can occur, especially with heavy, clay-based soils or poor watering habits. Fungal and bacterial buildup increases if the substrate doesn't dry out between waterings.

How to identify root rot in cannabis plants

Identifying root rot early can make the difference between saving your cannabis crop and losing it entirely. Fortunately, cannabis root rot symptoms are often visible if you know what to look for, especially when it comes to hydro setups where the roots are exposed. Whether you're growing in soil or hydro, careful observation is key.

Early warning signs

The first signs of rotting roots often mimic general plant stress, but escalate quickly:

• Drooping or wilting plants (even when properly watered)
• Yellowing or curling leaves (especially at the bottom)
• Brown, slimy, or mushy roots
• Stunted growth or nutrient deficiencies
• Weak or floppy stems

Cannabis leaves affected by root rot may also show symptoms, such as pale blotches, burnt tips, or sudden loss of rigidity. If your plants appear overwatered but the schedule hasn't changed, root rot could very well be the silent cause.

Visual inspection tips

To confirm root rot, closely inspect your plant's root system, especially in hydroponic setups, where access is more straightforward. As mentioned, healthy roots should appear bright white or cream colored, feel firm to the touch, and have little to no smell. In contrast, infected roots often turn brown, become soft and visibly slimy, and may clump together or disintegrate when handled.

Always check the smell, as a foul, swampy odor, similar to stagnant water or rotten eggs, is a clear indicator that the root rot has taken hold in your system. If you're still unsure whether the issue is root rot or another disease, consult our comprehensive guide on how to identify and treat cannabis plant diseases for more insight.

Root rot symptoms in hydro vs soil cannabis setups

By now, it's clear that cannabis root rot isn't limited to one growing setup. However, how it manifests and the proper course of action vary significantly depending on your growing method.

Root rot in hydroponics

Hydroponic systems offer plenty of benefits but are particularly susceptible to root rot if not properly maintained. In hydro grows, the root system is typically suspended in water, making oxygen deprivation and pathogen buildup likely in improper conditions. If water becomes stagnant, unsterile, or too warm, bacteria and fungi like Pythium can take hold quickly.

Some specific symptoms of root rot in hydroponics include:

• Rapid plant drooping, even when nutrients and pH are normal
• Roots that turn brown and slimy almost overnight
• Bubbles or foam forming in the reservoir
• A strong, unpleasant odor from the root zone

Since the roots are visible in hydro, identifying rot is more straightforward: just lift the lid and check.

Root rot in soil

In soil setups, root rot cannabis symptoms may be slower to appear, but can be just as damaging. Overwatering and poor drainage are the main culprits here, as they create anaerobic conditions that suffocate roots and promote fungal growth.

Common signs in soil-grown cannabis include:

• Slow, progressive yellowing or curling of lower leaves
• Soil that stays wet for too long or smells sour
• Weak, spindly growth and frequent signs of nutrient lockout

Unlike in hydro, inspecting the roots in soil requires carefully removing the plant from its container. If you notice root rot in cannabis leaves paired with soggy, compacted soil, rot is likely the cause.

How to fix root rot in cannabis

If you've confirmed cannabis root rot, the good news is that recovery is possible, especially if you act fast and precisely. Whether you're dealing with hydro or soil, the key is to remove the source of infection, restore root health, and adjust your environment to prevent future outbreaks.

Remove affected roots

Start by gently removing your cannabis plant from its pot (soil) or reservoir (hydro) and carefully wash away any debris with lukewarm, filtered water. Examine the root system closely. Use sterile scissors or pruning shears to cut away all mushy, brown, or foul-smelling roots; these areas won't recover and only risk spreading the rot further.

Be thorough but cautious. Only keep firm, pale roots that show signs of life. Dispose of infected root matter immediately, and sanitize your tools after use to avoid cross-contamination.

Treat with H₂O₂ or beneficial bacteria

Once the damaged roots are trimmed, treat the healthy remainder with either hydrogen peroxide (H₂O₂) or beneficial microbes, but not both at the same time.

• Hydrogen peroxide: In hydroponics, a mild solution of food-grade H₂O₂ (typically 3%) helps to sterilize the root zone, killing off lingering pathogens. However, it can also kill beneficial bacteria, so be sure to use it selectively.
• Beneficial bacteria or fungi: In hydro and soil, products containing mycorrhizae or Bacillus subtilis introduce friendly microbes that outcompete pathogens and promote root regrowth. These are especially effective in organic grows or when used after peroxide treatments have fully cleared.

Applying the proper treatment boosts root resilience and helps restore a balanced microbial environment.

Improve oxygenation and drainage

Root rot thrives in oxygen-deprived environments, so improving air and drainage is essential to full recovery.

• In hydroponic systems: Add or upgrade your air stones, pumps, or circulation systems to keep water moving and highly oxygenated. Maintain water temperatures below 70°F to slow pathogen growth.
• In soil grows: Replant into a fresh, well-draining medium like coco coir or a perlite-rich soil blend. Avoid compacted or peat-heavy mixes that retain excess moisture. This step is critical in fixing root rot in the soil in the long term.

By restoring proper airflow and removing the conditions that allowed root rot cannabis issues to develop, you give your plants the best chance to rebound.

Preventing root rot in the future

After dealing with cannabis root rot, prevention is the most powerful tool in your arsenal. Once you've nursed your plants back to full health and stabilized the growing environment, you'll want to ensure that root rot doesn't return, especially in future cycles. The good news? By building a healthier root zone and improving your growing habits, you can dramatically reduce the risk of reencountering root rot.

Below are some key strategies for future-proofing your grow and maintaining strong, resilient roots that will see you through to a fruitful harvest.

Control watering habits

Overwatering is one of the most common mistakes growers make, especially in soil. To avoid waterlogged conditions that invite root rot cannabis problems, adopt a measured, responsive watering schedule. Allow the top layer to dry out between waterings, and make sure pots have sufficient drainage to avoid overwatering.

For further guidance, see our full article on how to water cannabis plants the right way.

Increase oxygen and airflow

In hydroponic setups, ensure your reservoir is well-aerated by using top-quality air stones and pumps. Keep water temperature within the ideal range of 65–70°F to boost dissolved oxygen and reduce the risk of harmful microbes taking hold. In soil, consider adding perlite or coco coir to improve aeration and structure.

Good airflow above the canopy also supports overall plant health and helps prevent secondary issues like mold or mildew.

Use mold-resistant strains

Some strains are simply better equipped to deal with damp environments. If you're growing in a region with high humidity or you've struggled with root rot in the past, starting out with the right genetics can make a huge difference.

Explore our list of mold-resistant strains to give yourself a head start in disease prevention.

Maintain ideal humidity levels

Root health and humidity go hand in hand. Excessive humidity and moisture create conditions that promote fungal outbreaks, not just at the roots, but throughout the plant. Invest in a hygrometer and monitor your grow room's relative humidity, especially during flowering.

Learn more about how to maintain humidity when growing cannabis, and why it's a crucial part of disease prevention.

Rewarding results without root rot

Root rot can be an alarming discovery, but it's manageable with the proper knowledge and quick action. By recognizing early signs like drooping leaves, brown or mushy roots, and foul aromas, you can step in before serious damage occurs. Knowing how to fix root rot in hydro and soil, from trimming damaged roots to improving oxygenation, can bring your plants back from the brink. By adopting some smart prevention strategies such as better watering habits, increased airflow, and choosing mold-resistant strains, you can avoid root rot altogether in future grows.

Bookmark this guide and share it with fellow growers to help keep more cannabis plants healthy and thriving. And if you're ready for a fresh, resilient start, browse our full selection of premium cannabis seeds to kick off your next grow with confidence.