How to Fix Rust Spots On Leaves During Flowering

If you’ve been noticing reddish-orange spots on your cannabis leaves lately, your marijuana plants could be suffering from leaf rust or rust-colored spots – especially rust spots on leaves during flowering. 

Hold on, you may be asking how do plants rust?

Obviously, rust spots on cannabis leaves are not the same type of rust that occurs on metal objects. Instead, rust-colored spots on your plant are caused by either:

  1. a type of disease from a pathogenic rust fungus; or,
  2. a nutrient deficiency of magnesium or calcium.

Rust fungus manifests by creating a powdery rust-colored deposit on the leaves. Sometimes, the fungus leaves behind little brown spots or a dark brown edge on the leaves.

While rust spots generally don’t kill the plant, it certainly does have other unwanted side effects – which we discuss later on.

Diseased Cannabis Leaves During FloweringPin

Removing rust fungus o rust spots on leaves during the flowering phase can be a real challenge. If you’ve recently caught your cannabis plant’s leaves developing telltale signs of rust spots, don’t worry.

This article seeks to explore everything you need to know about rust spots on leaves during flowering.

Also, as indoor growers, what preventative measures we can do any further rust fungus problem from spreading to remaining plants in your grow space.

What Causes Rust Spots On Leaves During Flowering?

Rust spots are most likely caused by a fungus, and sometimes by nutrient deficiency. It can be a headache for all indoor growers.

Rust spots can affect indoor growing environments, light-enabled environments, and outdoors in a raised garden bed.

It has the ability to infect thousands of plant species, and the fungus-caused rust spot will appear during the flowering phase and can ruin an entire harvest. 

Rust Fungus Causing Rust Spots

Rust fungus is caused by a special fungal parasite that only affects plants. Its scientific name is Pucciniales (also known as Uredinales)[1].

However, unlike some other forms of fungi, which decompose living organisms, rust fungus only affects living plants, not dead matter.

This is the reason why the parasite allows the plant to stay alive but at the same time causes damage so the plant can’t absorb nutrients properly.  

Nutrient Deficiencies

Apart from a fungal infection, these kinds of rust spots generally tend to be caused by a magnesium or calcium deficiency (or possibly nutrient burn).

However, in most cases, the root cause of rust spots is fungus or rust mold.

How To Identify Rust Fungus On Leaves

Plant rust occurs when the external environment is heavily laden with moisture and dampness.

Like most plant-based parasites, rust fungus attacks plants when exposed to dank conditions for too long. 

This infection is spread through the production and distribution of fungal spores.

So, if a single infected cannabis leaf contains these spores, it can easily spread to nearby leaves within the same plant or even spread the disease to plants in the vicinity. 

The fungus is spread by air and water. Wet surfaces are essential for the parasite to multiply.

This is why you’ll often find an increased occurrence of rust spots across your plants after watering them with plain water. 

Here’s how to figure out whether or not your plants have rust spots:

  1. Can you see a white or yellow leaf spot forming on your plant’s upper or lower leaves or lower branches?
  2. You may also find orange or yellowish colored spots or streaks underneath the affected leaves.
  3. Look for pustules on the underside of these leaves. Pustules are small, blister-like bumps that usually range from orange to brownish red in color.
  4. Don’t confuse rust fungus with leaf septoria. Leaf septoria also causes leaf spotting but is caused by another type of fungus called septoria lycopersici. It is also a destructive disease that is most severe when it is wet or in high humidity areas for long periods of time.
  5. In more advanced stages of the infection, you’ll notice those reddish-brown spots across the plant’s leaf surfaces. These spots will often boast a powdery complexion and are often accompanied by fungal reproductive spores.
Fixing Rust Spots On Leaves During FloweringPin

Any weed plant suffering from rust will boast these signs and other symptoms.

The exact symptom will depend on how far the infection has progressed. In the final, most advanced stage of infection, you’ll find those signature reddish bumps infecting the majority of the leaf surface.

To determine if these spots are a sign of an infection or nutrient burn, rub a spot with your fingers.

If the rust rubs onto your fingers, it’s an infection. If not, it’s a nutrient burn.

Is Rust Fungus on Cannabis Leaves Harmful?

As previously noted, the fungus isn’t going to kill your marijuana harvest.

The parasite needs an organism to stay alive, hence serving as a continuous mode of nutrition for the fungal parasite to feed off. 

However, even though you don’t need to worry about your plants dying of a rust infection, you should still do your best to purge your plants of this unwanted pest.

If you allow plant rust to sit for too long on any one of your plants, you run the risk of infecting your entire garden.

While it’s true that rust spots don’t infect every plant species, they still can infect the majority of your plants.

Some plants are immune to a certain variety of the plant rust parasite but may develop an infection when exposed to another strain of the fungus. 

Regardless, you should start purging your infected plants of this parasite as soon as possible, or else it may transfer onto the remaining plants and cause an infection there, too.

If this happens, you’ll need to start growing new plants.

Marijuana leaf that has rust spotsPin

The plant rust parasite spreads notably fast thanks to its spores.

These spores are remarkably sturdy and can’t be destroyed by extreme temperatures, flooding, or infection thanks to their hardy chitinous external layer.

This is a signature feature of all fungal spores, making them excellent at resisting external danger.

Still, despite its tough spores, leaf rust fungi can be completely removed from your cannabis crops as long as your employ the right methods. 

Before we dive into rust control and prevention methods, though, here is a list of reasons why plant rust can be harmful to your marijuana plants:

  • Rust infections can cause your leaves to weaken and turn yellow. Eventually, they can cause your plant to start shedding leaves without killing it. However, when a cannabis plant loses its leaves, it loses out on energy-making bodies.
  • This is because your plant’s leaves are where the majority of photosynthesis and respiration take place.
  • When these two fundamental biological processes are compromised, your plant will weaken and go into survival mode. It will stop developing new leaves. Plant growth will also be severely stunted. 
  • Plants sometimes need extra water during the flower production phase.
  • When we water our plants too often without exposing them to enough sunlight, they will begin to rust. This is because rust thrives in damp conditions. Unfortunately, rusting cause your flowers to die out and fall off.  

Rust Fungus Prevention

If your cannabis plants are experiencing leaf rust, don’t worry.

We’ve got a list of techniques you can use to purge your plant from this harmful disease and a series of ideas that can help prevent the infection from developing in the first place. 

Yellowing brownish Marijuana LeafPin

While there isn’t a fixed, straightforward method to curing your cannabis plant, you can still try to control rust using these tips.

If you control the existing disease and prevent it from spreading to other plants, your grow room might be able to recover and grow back into its original healthy form:

  • Remove infected leaves and safely dispose of them.
  • If you leave them out in the open, they might still spread existing spores and infect your other plants in your grow room.
  • If you feel like the majority of your plant’s leaves have been infected by the fungus, it’s probably best to take a loss and throw it out.
  • Always disinfect your tools, too! A mild bleach solution does an excellent job of removing any fungal spores from your pruning tools.

If you’re looking for a pair of shears, we highly suggest these pruning shears. They are great for fine pruning and they are so sharp that cutting through plants is easy. Otherwise, we have a list of other pruning scissors to consider.

Fiskars Micro-Tip Rose Pruning Shears, 6" Garden Shears Non-Stick Coated Stainless Steel...
  • GARDENING ESSENTIAL: With these stainless steel blade gardening shears,...
  • MAXIMUM POWER AND PRECISION: Micro-tip blades on these garden clippers...
  • LONG-LASTING AND RELIABLE: Stainless steel blades stay sharp through heavy...
  • When buying new plants, always use rust-resistant seed varieties. These special GMOs can keep your crop safe from the rust parasite.
  • Avoid splashing water on your leaves as rust fungi love dampness and grow well in wet conditions.
  • Make sure your crops are getting enough light exposure so that any excess water evaporates away.
  • Maintain ample distance between your crops to prevent excess moisture retention in the surrounding air.
  • If the rust occurs due to a calcium deficiency, increase the amount of the lacking nutrient.
  • Some plant and flower nurseries stock rust fungicides. You can try using those to purge this parasite off of your plant. However, these fungicides can sometimes have negative side effects. We recommend natural remedies such as using natural sprays such as garlic spray, sulfur spray, and copper spray.

We recommend this copper fungicide as it has completely gotten rid of the rust fungus for us.

Bonide Captain Jack's Copper Fungicide, 16 oz Ready-to-Spray Disease Control for Organic...
  • Control fungus and disease in your garden with Captain Jack’s...
  • Approved for organic gardening, this fungicide is suitable for the...
  • Copper Fungicide effective in the control and prevention of a wide range of...

Successfully employing these methods can help you control rust spots on the leaves, especially during the flowering season when your harvest will require extra water.

If you allow the rust to keep growing, you may reach a point where you’ll need to invest in all-new plants. 

Rust Spots Caused by Calcium or Magnesium Deficiency

Rusty brown spots can also be a sign of a magnesium or calcium deficiency or more than likely a lack of magnesium than calcium.

Generally speaking, minor nutrient deficiencies won’t affect the flowering of your weed plants, but once they flower, the resultant deficiency will worsen.

This is because the plant needs more nutrients in the flowering stages.

Nutrient deficient Marijuana LeavesPin

However, if you are doing address the mineral deficiency, it will worsen.

The rust spots will continue onto the middle-aged leaves (those slightly below the upper leaves of the plant) and spread quickly to all the remaining leaves.

This results in a lower production of flowering.

You need to treat the nutrient deficiency immediately. If not, it leads to a plant being unable to uptake calcium and magnesium.

This condition is called “nutrition lockout” (we address this later on).

How to Find Out if It’s A Nutrient Deficiency

First, make sure that the rusty spots are indeed the result of the plants not getting enough magnesium or calcium.[2]

This can be the result of not feeding the plant enough, or because the nutrients are locked out. To determine what the cause is

You’ll need to look at the symptoms that are common to a deficiency of magnesium or calcium.

Symptoms Of Magnesium or Calcium Deficiency

When the plant leaves begin to curl, this is an indication that the plant lacks calcium.

However, if the leaves begin to turn yellowish but the veins stay green, this is a clear sign that the plant is not receiving insufficient magnesium.

Nutrient Deficient Cannabis LeavesPin

In either case, you will need to provide your plant with more nutrients.[3]

However, if you give you are providing enough different nutrients to your plant and the symptoms don’t resolve themselves, the problem is that the plant is simply not able to absorb the nutrients.

What is Nutrient Lock Out?

Nutrient lockout is simply when a plant is unable, for whatever reason, to absorb and feed itself all nutrients from the soil.

There are several reasons for this, but the most common issue is the varying pH level in the soil.

Minerals and nutrients have varying degrees of pH levels where they are absorbed the best.

If the ph levels are outside a certain range, the mineral or nutrient is unable to be digested by the plant – no matter how much you feed the plant. The nutrients are simply locked out.

For weed plants, the soil pH level should be maintained at 6.8 to 7.2. So first, check the soil pH levels.[4]

Personally, we like this pH meter. It’s not expensive and it’s accurate enough for the everyday weed grower.

VIVOSUN Digital pH and TDS Meter Kits, 0.01pH High Accuracy Pen Type pH Meter ± 2%...
  • Application: Great for all home and laboratory TDS & pH testing...
  • PH Meter: Full measurement range of pH 0 - 14, reliable and quick readings
  • 3-in-1 TDS Meter: Measurement Range 0-9990ppm, 0-9990µs/cm; Accuracy ±...

If the soil pH level is in the correct range, then other possibilities for nutrient lockout are:

  • the growing environment is too wet or cold, or
  • the ratio of other minerals such as ammonia, potassium, or the balance of calcium and magnesium is not quite right.

With that said, if your plant is locking out magnesium or calcium uptake, other nutrients will be locked out as well.

So, if you fix the magnesium or calcium issue, you will also be solving other nutrition deficiency issues.

How to Fix Nutrient Deficiency Issues

First, check the pH level in the soil to rule this out. You can easily test pH levels in the soil by getting a pH meter.

Soils with pH levels around 6.8 to 7.2 are the best for both calcium and magnesium uptake.

After testing the pH level in your soil and it’s far off from this range, then it’s likely that is the reason for your nutrient deficiency.

If the pH level in your soil is acceptable, then the simple answer is that you need to provide more nutrients to your plants.

How to Fix Rust Spots On Leaves During Flowering | UrbanOrganicYield.comPin

Nutrient Burn

If the issues you face are not a fungus or nutrient lockout, the third problem might be nutrient burn. This basically means there are too many nutrients.

To resolve this issue, you need to flush the nutrients out of the tap water.

Simply, add tap water to your soil to flush out all the nutrients. Once you give it a good flush, there should be very little nutrients in the soil.

You will want to add a little nutrient back into the soil.

Otherwise, you will start to notice your plants beginning to droop. We suggest giving your plants half the amount they were getting before and monitoring them closely.

Why Does My Cannabis Plant Have Rust Spots?

Cannabis plants have rust spots for two reasons, either it’s caused by a type of pathogenic rust fungus or rust spots could be caused by a nutrient deficiency in either magnesium or calcium.

How Do You Treat Rust Fungus?

To treat rust fungus, you need to first cut off and get rid of all infected portions of the plant. Make sure you throw them away as they can infect other plants in the area. Second, clean all debris in and around the plants. between plants to prevent rust from spreading. Next, you can apply a copper fungicide to get rid of and prevent future infections. However, if there is too much rust fungus on your plant, it might not be able to be saved.

How do you get rid of Plant rust naturally?

A weekly sulfur dusting can help to treat rust fungus. Rust can also be managed by applying Neem oil or another botanical fungicide. Another homemade and natural fungicide is to make a spray by combining baking soda with light horticultural oil. With DIY sprays, you can control the strength and concentration of the spray.

What Causes CalMag Lockout?

Nutrient lockout (or CalMag lockout in the case of calcium and magnesium) occurs when the soil or growing medium in a garden is overly saturated with excess nutrients. This could be due to overfertilization or high salt content. When plants are incapable of absorbing essential nutrients such as calcium and magnesium, they are unable to absorb nutrients, which leads to plant disease.


To successfully grow indoors and outdoors, growers will need to be on the lookout for rust spots on their weed crops.

Use the methods described in this article to determine if your rust spots are caused by fungus or by a lack of nutrients.

Hopefully, you’ll be able to fix rust spots on your leaves that happen during the flowering process.

By doing so, you should be able to increase your crop yields or save the rest of your harvest from getting rust spots.

If you have any other questions, please do leave a comment below and we’ll try to get back to you.

Other Common Growing Issues

Along with rust spots, growers also face other issues from septoria to calcium deficiencies. Read more on our related posts on other common issues that indoor growers face. Read more on our related posts:


Show More

Leave a Comment

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Share to...