Root Rot

The origins of root rot in your hydroponic system lie in both an imbalance of organism/pathogens and lack of system oxygenation and/or uncleanliness. Because hydroponic systems are normally active w/irrigation and reservoirs feeding tables or buckets or simply drip systems. Anywhere there is water and roots invites the ability to develop root rot. Here we will specifically be discussing hydroponic systems.

Whether you use a reservoir or aeroponics or DWC/RWC the health of your plants is directly tied to these nutrient delivery systems. So when you see brown slimy roots, and oily brown film in your tanks, filters or tables its important to react quickly.

Root rot is generalized term for a number of plant pest like fungi, virus, pathogen, bad bacteria, dampening off, bio mass decay and because it can be a number of things and maybe multiple not everyone’s source will be the same. 

There are even water molds that can travel from one plant to another using adapted appendage to find new host plants and host environments to feed on and multiply. 

When we are identifying root rot we often see other signs of general plant stress, curling, spotting, burning, chlorosis, slight deficiencies, wilting plants, stunted growth and sometimes plant randomly die. When in later stages of development like bloom, root rot can lead to sever deficiencies causing buds at any stage to wither and die. 

The first sign of root rot in hydro cannabis plants (besides brown roots) is usually wilting


Brown Slimy Roots starved of oxygen and coated with a film that allows pathogens to easily multiply and blocks out oxygen. Lots of free flowing dissolved oxygen is neccsary for  a healthy hydroponics sytem but as you can see here even  a healthy system is now not going to be working optimally.

These cannabis roots are brown with root rot - they're slimy, smelly, and will kill your plant if not treated immediately!

Burnt Leaves mimicing water, heat and/or pest damage.

Example of a sick cannabis leaf caused by root rot

Cannabis roots just got root rot - brown roots and leaves are wilting - often triggered by heat

Here you can see root rot can exist in clean water, above the water line or below. The Difference between the affected and unaffected roots is apparent, as healthy roots are white with axillary/lateral branching.

Sometimes it's only the roots above the water that are being affected, and the roots in the water itself are still relatively healthy

If you have a dirty system and/or can see visible slime and brown unhealthy roots the first step is to usually clean the system. The oily film you see in your reservoir is also coating you roots and preventing oxygen from reaching them adding to the build up of toxic pathogens, bacteria or fungi. As roots die they begin to decay stealing even more oxygen from the environment and causing further issues and pH imbalances. 

Slimy, snotty cannabis roots with a bad case of root rot and possibly an algae bloom

It is important to differentiate between nutrient stained roots and root rot. You do not want to potentially disturbe a healthy root system if not needed.

Cannabis plant - roots are brown because they're stained from nutrients, not because of root rot!

Nutrient stained roots won’t be slimy or smell, there won’t be an oily film and will appear healthy other then color. 

Correcting a root rot issue from one or many sources can be achieved through a treatment and/or normal cleaning and maintenance routine.

Its important to note not all damage will repair, roots will regrow but almost dead or weak/wilted stalk and buds, leaves probably repair and should be removed. Same with the dead or decaying material that can possibly enter your reservoir’s.

These cannabis roots are brown with root rot. Sick roots often look wound up or twisted like this, and the individual "strands" sort of meld together with slime

In a hydroponic system your roots and the solution they sit in need tremendous amounts of oxygen to both feed your plants and keep a system balanced. A hydroponic system that is lacking in oxygen is an inviting environment for the plant pest that cause root rotCannabis plant drooping due to root rot

Prevention is as simple as cleaning all your equipment thoroughly, try to not disturb established root system and keeping it and anything that goes into your system clean. White ivory roots quickly become brown and slimy as root rot takes over and plants infected with viruses or fungi will quickly wilt and die.

The burnt discolored leaves of a cannabis plant with root rot

Burnt leaves and tips with necrotic patches all over.This is an example of what cannabis leaves can look like after the plant starts suffering from cannabis root rot

Bud termination and dry down

A cannabis plant affected by root rot - leaves are turning brown, discolored, burnt white tips and edges, curlingA cannabis plant affected by root rot - leaves have spots, burnt yellow tips and edges, curlingDamage caused from pathogens and fungi from root rot is often permanent. 

Preventative measures to root rot are as follow

  • Keep room/system clean 
  • Keep hydroponic system cool (64-70 Degress)
  • Maintain a cyclic maintenance and water change schedule after a 2-4wk incubation period 
  • Leave healthy root systems alone
  • Use beneficial bacteria … Bacillus and Pseudomonas spp Beneficial bacteria, like beneficial fungi, form a symbiotic relationship with the plant insulating them from damage as well as enabling better nutrient absorption 
  • Clean anything that enters your system, prior to use.

A gross, slimey case of brown roots - caused by a pathogen known as "root rot." Yuck!

Knowing what to look for will help with choosing a course to correct your issues.

 Beneficial Root Bacteria – Crucial!

Adding beneficial bacteria to your hydrosystem will help prevent and treat root-related plant diseases and help make nutrients available to the plant. Some of the formulas available are HydroguardPiranhaVooDoo JuiceGreat White (Great White has great reviews, yet is obscenely expensive), Subculture BRooters, and Plant Savers.   Great white and Hydroguard together form a multifaceted system booster/inoculant tfor hydro system health to ward off pathogens and viruses and increase plant health.

Botanicare HydroGuard is a great treatment and preventative for marijuana root rot

The active ingredient in Hydroguard is a specific type of bacteria called Bacillus amyloliquefaciens. It survives in hydroponic reservoirs better than other types of Bacillus bacteria and fights many root ailments including different types of fungi, bacteria and oomycotes. It not only gets rid of and prevents root rot, but there’s some evidence Bacillus a. may actually help lower salt concentration in the plant tissue itself!

Maintain a highly oxygenated environment 

As I mentioned, it is incredibly beneficial to try to get as much oxygen as possible dissolved in your water. Therefore it’s a good idea to buy a BIG air pump and big air stones for your hydroponic system.

Up to a point, the more bubbles and surface agitation, the better, as this dissolves more oxygen into the water. As long as the roots are not being very disturbed, you can’t really go wrong with adding more oxygen.

The source of your root rot in general has a much harder time establishing in an oxygen-rich environment and your plants will grow faster with lots of oxygen. 

I use one EcoPlus 2 Air Pump w/ 2 Outlets for each 10 gallon container (which each hold 6 gallons of water), which I have connected to 2 large air stones per air pump (since this one 2 outlets – this helps make sure there’s plenty of oxygen in the water healthy roots and faster growth).

Get a large airstone on Amazon to make lots of bubbles!Get a large airstone on Amazon to make lots of bubbles!3/16" Flexible Airline Tubing for AquariumsGet a EcoPlus 728360 3W 2 Outlet Eco Air Pump, 126 GPH on!

Make sure there are lots of bubbles in your plant reservoir to help protect your cannabis from root rot!

Keep grow room cool, keep your hydro system cool 

Since more than a few causes of root rot are plant pathogens and viruses maintaining a healthy environment free from stress is optimal. This means controlling temp and humidity

In an ideal world, the maximum recommended temperature for the water in your reservoir is around 72°F (22°C) and some growers will go to great lengths to keep their reservoirs very cool. 

Top off reservoir for first few weeks, without doing a full reservoir change until after roots are well established.

When it comes to nutrients and plant growth in a hydroponic setup, it’s important to change your reservoir water regularly. This is especially important in the flowering stage when the plant is very sensitive to nutrients and pH. Regularly changing your water every 7-10 days will help your plants get better access to nutrients, and help prevent deficiencies and toxicities.

However, when your hydroponic system is first getting established the solution doesn’t have an established colony of good bacteria around the roots, and has not yet grown a biofilm that protects the roots against pathogens.

Just like bad bacteria can create a film that will starve your roots good bacteria will create a film that protects your roots this is why disturbing a healthy roots system can create a root rot issue.

Its recommended for the first 2-4 weeks just top of your reservoir untill roots are fully established to encourage healthy bacteria forming.

 Keep Everything Clean

Clean air clean room, clean equipment. Anything that enters your system should be sterile and clean. 

Eliminate Light leaks to your hydro system

Any plastic or lines or reservoirs should be black and/olr are light proof as to not allow light of any kind to interact with your hydrosystem. This is an often over looked point and is all that is necessary to completely negate an entire Root rot response or preventative efforts. 

Don’t let any light get to your roots or reservoir water, as it provides heat and light which will promote the growth of algae and bacteria (and not the good kind).

Hydrogen Peroxide (H2O2) Is Only a Temporary Solution

Don't use H2O2 for cannabis root rot - it's temporarily effective at best

Don’t use H202 unless you are starting out, H202 will reset your entire system and make it much harder to get back to where you were before using H202




Botanicare HydroGuard is a great treatment and preventative for marijuana root rot

I recommend  using Botanicare Hydroguard and great white root inoculant to correct and prevent root rot. The below photos are treatment with just Hydroguard, adding great white will keep root rot at bay and create a healthy system. 




Canabis plant with root rot - hydroponics - deep water culture DWC

Cannabis roots just got root rot - brown roots and leaves are wilting - often triggered by heat

Roots are beginning to recover

This cannabis plant is beginning to recover from root rot - notice the new white roots growing out of the old sickly brown ones

Roots are now mostly recovered below

Root rot in cannabis - post recovery

Using hydroguard and Great white at label rates as well as keeping a clean room and optimal environment will help prevent and control root rot and root rot issues. It is surprisingly effective even in hot, unclean reservoirs. Hydroguard and Great white will defiantly get you through initial problems or outbreaks and help prevent new issue from arising.

A closer look at root rot in cannabis in a hydroponic DWC setup

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