Root rot in cannabis turns healthy white roots brown, slimy and foul-smelling, and the plant above droops, yellows and stops growing no matter how you water it. It’s usually caused by water molds feeding on roots that are short on oxygen. Cool and aerate the root zone, clean the system, and add beneficial microbes to stop it.
Root rot isn’t a single disease. It’s a name for root decay caused by a handful of pathogens, most often Pythium, a water mold that thrives in warm, low-oxygen water. Fusarium and Rhizoctonia fungi can cause similar damage, especially in soil. They all take advantage of stressed roots, so root rot is really a problem of conditions first and pathogens second. It’s most common in hydroponics, but soil and coco plants get it too when they stay soggy. For the background on where these organisms come from, read our article on where root rot comes from, and see the root problems page for other root issues.
Cannabis root rot symptoms
The trouble with root rot is that the first signs show up above the soil line, where they look like a dozen other problems. Check the roots before you change your feed.
- Brown, tan or gray roots instead of white or cream
- Roots that feel slimy and slide apart when you pinch them
- A sour, swampy or rotten smell from the root zone or reservoir
- Brown film or sludge in the reservoir, tubing or tray
- Drooping that doesn’t recover after watering or with the lights off
- Yellowing leaves and brown, burnt-looking edges and spots
- Stunted growth and, in late cases, sudden collapse
In flower, root rot can starve buds of water and nutrients, so they stall or never fill out.
What healthy hydroponic cannabis roots look like
Healthy hydroponic cannabis roots are bright white to creamy, firm and fuzzy with fine root hairs. They smell clean or earthy. Some nutrients and additives can tint roots tan or brown, so color alone can fool you. The pinch test and the smell are the real giveaways. Healthy roots, even stained ones, stay firm and smell fine. Rotting roots are mushy, slimy and stink.
What causes root rot in hydroponics and soil
- Warm water. Once reservoir water climbs above about 72 °F (22 °C), it holds less oxygen and Pythium grows faster. Our article on the ideal temperature for a nutrient reservoir goes into detail.
- Low dissolved oxygen. A failed air pump, clogged air stone or too little aeration in DWC suffocates roots fast.
- Overwatering. In soil and coco, a medium that never dries out drives oxygen out of the root zone. See our page on overwatering cannabis.
- Dirty systems. Leftover organic matter, dead roots and biofilm in tanks and lines feed the pathogens.
- Light leaks into the reservoir. Light grows algae, which uses oxygen and gives pathogens more to feed on.
- Infected plants or water. Sick clones, contaminated tools and untreated water can introduce the pathogens.
How to treat root rot in cannabis
1. Cool the root zone
In hydro, bring the reservoir down to about 65 to 68 °F (18 to 20 °C). A water chiller is the dependable fix. Frozen water bottles can help in a small system for a short time, but don’t let the temperature swing wildly.
2. Increase oxygen
Add air stones or a bigger air pump in DWC, and keep the stones clean. Make sure water moves in recirculating systems. In soil and coco, let the top of the medium dry before the next watering, and make sure pots drain freely.
3. Clean or swap the reservoir
Pull the plants, dump the nutrient solution, and scrub the reservoir, lines and air stones to remove slime and biofilm. Rinse well and refill with fresh, pH’d solution. Block every light leak into the tank.
4. Trim dead roots
With clean scissors, cut away the brown, mushy roots and leave anything firm and white. Rinse the remaining roots gently in clean, cool water before putting the plant back.
5. Choose microbes or peroxide, not both
Beneficial microbes, such as Bacillus bacteria and Trichoderma fungi, compete with pathogens and colonize the roots. Hydrogen peroxide oxidizes pathogens in the water. The catch is that peroxide also kills beneficial microbes, so pick one approach at a time. If you use peroxide to clean up an outbreak, wait until it has broken down and then add beneficials to recolonize the roots.
| Treatment | Best use | Watch out for |
|---|---|---|
| Beneficial microbes | Ongoing protection and recovery | Killed by peroxide and other sterilizers |
| Hydrogen peroxide | Short-term cleanup of an outbreak | Too strong a dose damages roots; follow the label |
| Chilled water | Every warm hydro setup | Avoid big temperature swings |
| Better drainage | Soil and coco | Water less often, not just less per watering |
6. Watch new roots
Recovery shows up as fresh white root tips within a week or so. If the brown roots keep spreading after you’ve cooled and aerated the system, the infection may be too far along, and a badly hit plant can be a risk to the rest of the garden.
Root rot in DWC
Deep water culture is where we see root rot most. The roots sit in water full time, so anything that drops oxygen, such as a warm room, a failed pump or a crusty air stone, hits the plant within a day. Check reservoir temperature every day, keep a spare air pump on hand, and change the solution on a regular schedule. Our guide to water culture hydroponic systems covers setup basics.
Problems that look like root rot
| Problem | What you see | How it differs |
|---|---|---|
| Overwatering | Droopy, heavy leaves | Roots are still white and firm, and the plant recovers once the medium dries |
| Underwatering | Limp, thin leaves | Medium is dry and the plant perks up within hours of watering |
| Nitrogen deficiency | Yellow lower leaves | No drooping or root damage, and yellowing moves up from the bottom |
| Heat stress | Curling, burnt-looking top leaves | Leaves near the light suffer most, and the roots look healthy |
Still unsure? Work through the symptoms in the Cannabis Doctor.
How to prevent root rot
- Keep reservoir temperatures in the mid to high 60s °F (about 18 to 20 °C).
- Run plenty of aeration and keep spare pumps and air stones ready.
- Make reservoirs and lines light-tight.
- Clean and sanitize the whole system between runs.
- Use beneficial microbes from the start in hydro.
- In soil and coco, use pots that drain well and let the medium partly dry between waterings.
- Quarantine new clones and check their roots before they join the garden.
Frequently asked questions about root rot in cannabis
What does root rot look like on a weed plant?
Above ground, the plant droops even when it’s been watered, the leaves yellow and brown at the edges, and growth slows or stops. Below ground, the roots turn brown and slimy, fall apart when pinched and smell rotten. Healthy roots are white or cream, firm and clean-smelling.
Can a cannabis plant recover from root rot?
Yes, if you catch it early. Cool the water, add oxygen, clean the system, trim the dead roots, and add beneficial microbes or a peroxide treatment. You’ll know it’s working when new white roots appear. Plants with most of their roots gone often don’t recover fully.
What causes root rot in hydroponics?
Warm water, low dissolved oxygen and a dirty system are the main causes. Water above about 72 °F (22 °C) holds less oxygen and helps water molds like Pythium grow. Light leaks, dead organic matter in the reservoir and failed air pumps make an outbreak much more likely.
Can you use hydrogen peroxide and beneficial bacteria together?
Not at the same time. Hydrogen peroxide kills beneficial bacteria and fungi along with the pathogens. If you use peroxide to clean up an outbreak, let it break down first, then reintroduce beneficial microbes so healthy organisms recolonize the roots before pathogens can come back.
How do you fix root rot in soil?
Stop watering until the top of the soil dries, and make sure the pot drains freely. If the soil is waterlogged and compacted, transplanting into fresh, airy mix can help. Water less often, keep root zone temperatures moderate, and add beneficial microbes to help the roots recover.
Still not sure what’s wrong with your plant?
Members can post a photo in the Growing Exposed forums and get help from growers who’ve pulled their gardens back from root rot. Members also get the full video library, where we walk through real gardens and the problems growers hit along the way. See membership plans.