Rust Spots On Leaves During Flowering: Causes & Treatment

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If you are growing cannabis plants, then there are many things that you need to look out for. Every growth factor can have an outcome on the health of your weed plant.

One thing that you may notice is that your weed plant has rust spots on the leaves during flowering. So, what causes these rust spots on weed leaves, what are they, and how do you deal with them?

The three most common causes of rust spots on weed plants are rust fungus, nutrient burn, and calcium and/or magnesium deficiency. While rusty spots do commonly appear during flowering it is something that can actually occur during all growth stages.

Let’s take a closer look into each of the three causes and look at some important treatment and prevention tips that you really need to know.


Why Your Plants Have Brown Spots On Leaves During Flowering

rust spots on leaves during flowering

There are three common causes of rust spots on your marijuana plant’s leaves during flowering. These include rust fungus, nutrient burn, and calcium/magnesium deficiencies.

Let’s take a closer look at each of these issues right now to see what causes them, how to treat them, and how to prevent them from occurring in the first place.

1. Rust Fungus

weed leaf with rust

One of the most common causes of those brown spots on your weed plants is rust fungus. The fact of the matter is that rust fungus can affect weed plants just like any other plants. Rust fungus is a fungal parasite, one that affects only plants.

The scientific name for rust fungus is Pucciniales or Uredinales. The interesting thing about rust fungus is that it only affects living plants.

It requires living organisms to feed off of, unlike other fungi that can also grow on and feed off of dead plant matter. For this reason, weed plants affected by rust fungus will not die.

Rust fungus needs a living plant to survive, and will therefore not kill your plants. With that being said, the spores of this fungus rub off very quickly and also become airborne very easily even with the lightest of breezes.

This means that rust fungus spreads from one plant to another very quickly and easily. Rust fungus can cause the leaves of your marijuana plant to die and fall off.

This then results in your plant not being able to produce enough energy to grow properly. Although it won’t kill your plants, it can still negatively impact the health of them, so you do need to know what to do about rust fungus.

To determine if your plants have rust fungus, you can rub your fingers on those brown spots. If you see that some of that brown rust rubs off on your fingers, then you can rest assured that it is rust fungus.

Those are the fungal spores on your fingers. However, if it does not rub off, it is likely one of the other issues that we will discuss further below.

That said, these brown rust fungus spots can start out as white or yellow spots that form on the plants lower and upper leaves, as well as the lower branches.

It is also quite common to find yellow or orange spots or streaks under the affected leaves that have spots on the top. What you also want to look for are small pustules on the bottom of these leaves.

These are small bumps that can be brownish red or orange in color. during the more advanced stages of rust fungus infection, you will see reddish brown spots on many of your marijuana plants leaves.

These spots will feel powdery, and often have reproductive spores of the fungus present.

What Causes Rust Fungus?

The first step here is to determine what actually causes rust fungus in the first place. What you need to know here is that fungal spores are in the air all around us.

That said, it really all depends on the conditions in which your plants are grown. If you provide rust fungus with the right conditions, it can easily take hold and grow.

What causes rust fungus to take hold on your plants are all of the same conditions that any fungus needs to grow. Yes, those fungal spores are in the air all around us, but they need certain conditions, and the growing conditions in weed grow rooms are often suitable for fungus.

For one, these fungal spores have an easy time growing when the humidity is very high, and when temperatures are between 60 degrees and 80 degrees Fahrenheit.

These fungal spores have a very easy time taking a hold on plants when there is a high humidity level, moderate temperatures, and low air circulation.

If you don’t have good air circulation in your grow room, there is a good chance that some kind of fungus will grow.

Moreover, if you provide your plants with way too much water, thus causing the soil to be very wet, but you don’t provide them with enough sunlight to evaporate that water, then rust fungus can definitely occur.

The fact of the matter is that rust fungus is able to grow in the exact same conditions as marijuana thrives in. Therefore, being extremely diligent with your marijuana growth conditions is very important.

You want to do everything you can to minimize the chances of rust fungus from growing. As you will see below, there are a number of things that you can do to prevent rust fungus from taking hold on your marijuana plants.

How To Treat Rust Fungus?

As soon as you notice any rust fungus present, you need to remove all of the infected leaves immediately. Remember that those spores can easily spread from one leaf to another.

You want to immediately remove those leaves and get rid of them. Don’t put them in a trash can in the same room either. The best thing you can do is burn those leaves.

The only other thing that you can really do to get rid of rust fungus once it has started growing is to use some kind of fungicide. One of the best natural fungicides out there is sulfur.

Mixing sulfur with water and spraying your plants down will it likely kill the majority of the fungus present. Moreover, both baking soda and garlic also have the ability to kill rust fungus.

Mix these substances with water and then spray your plants down to kill fungus. If fungicide doesn’t get rid of the rust spots, then it is very likely that rust fungus is not the issue, but rather one of the other two issues that we will discuss below.

All of that said, the best thing that you can do here is prevention. Rather than treating an issue, it’s better to prevent it from occurring in the first place.

How To Prevent Rust Fungus?

There are a number of things that you can do to prevent rust fungus from taking hold on your marijuana plants.

Generally speaking, these are all of the same things that you would do to prevent any kind of fungus from taking hold in your marijuana grow room.

  • Always make sure that your marijuana grow room has great air circulation and ventilation. Yes, fungal spores do move in the wind, although this is not the issue here. The issue is that if your grow room is not well ventilated, it is likely that the humidity levels are going to be very high. Of course, high humidity levels often lead to fungal growth. Having good air circulation in the grow room will keep humidity levels down.
  • Not only do you want good circulation in the grow room, but also in between all of the plants. Therefore, always make sure that the leaves of your plants are not touching each other and that there is ample room between all of the plants. This will allow for good air circulation, and will therefore help keep humidity levels down.
  • Something else that can help keep circulation at a maximum and humidity levels lower is if you lollipop your cannabis plants. This is where you trim off the lower branches of your plant before it starts to flower. This will help increase air circulation.
  • Although you do of course need to water your marijuana plants, don’t give them too much water. If the dirt is constantly way too wet, it provides a great breeding ground for mold and fungus. Moreover, if you water the soil too much, that water is going to evaporate into the air, and also raise humidity levels to the point where fungus can easily grow. On that same note, you also want to ensure that you water your plants during the daytime, and not the night. If you water your plants during the night, the soil is going to stay wet for much longer, and therefore also provide a good breeding ground for mold.
  • Another thing that you can do to prevent mold and fungus from occurring is to keep temperatures at the lower end of the spectrum. Hot air holds more moisture than cool air, so having slightly cooler air will prevent high humidity levels from occurring.

2. Nutrient Burn

weed leaf with burn

If it is not rust fungus that is causing those brown rust spots on your plants, then it is likely that those brown spots are being caused by nutrient burn.

Yes, of course your plants do need fertilizers and various nutrients in order to grow properly. In fact, weed plants need quite a bit of nutrients. With that being said, there is of course such a thing as too much of a good thing.

Providing your plants with way too many nutrients can cause this nutrient burn to occur. Unlike rust fungus where the brown spots can rub off on your fingers, this is not the case with nutrient burn.

Yes, nutrient burn will cause brown rust colored spots. However, what is also very likely is that the tips of the leaves will turn yellow or brown.

Not only will they turn yellow or brown, but they will also look like they are drying out, and they will either bend or curl at the tips.

Moreover, if the main body of the leaves turn a super deep green color that appears to be oversaturated, then it is another indication that there is over fertilization occurring, with the result being nutrient burn.

Unlike with rust fungus, nutrient burn can definitely kill your plants, and it won’t even take that long to occur either.

What Causes Nutrient Burn?

Nutrient burn is caused by one thing and that is overfeeding your plants with bottled nutrients and fertilizers. Yes, you can still cause nutrient burn if you use natural products, although you would have to use a whole lot of them.

Using compost and back guano is very unlikely to result in nutrient burn, as they just aren’t strong enough to cause this. However, it is those bottled nutrients that you buy from your local grow stores that will definitely do the trick.

These nutrients are very strong and very concentrated. Using just a few milliliters too much can easily result in nutrient burn, especially if you are using an extremely concentrated product.

Too much nitrogen, phosphorus, potassium, and other micronutrients, in excess quantities, will all cause nutrient burn to happen.

How To Treat Nutrient Burn

What you need to realize with nutrient burn is that the damaged leaves will never fully recover. Those brown spots and the bent tips will not go back to their original shape or color. That damage is rather permanent.

However, you can prevent nutrient burn from progressing and damaging your plant further. If the nutrient burn has not already gone too far, there are some steps you can take to prevent it from getting any worse.

To resolve this issue, the only real thing that you can do is to flush the plant. By flushing the plant, we mean that you need to give it water that does not contain any nutrients.

You want to do this for at least a week, if not two weeks, in order to remove the majority of the excess nutrients from the soil. Besides removing excess nutrient levels from the soil and from your plant, there is really not much you can do to treat nutrient burn.

One thing that you can do is to clip off the damaged edges of the leaves, although this will not reverse any damage.

Due to the fact that damage cannot be reversed, it is essential that you move quickly as soon as you see any signs of nutrient burn happening.

How To Prevent Nutrient Burn

There are just a couple of things that you can do to prevent nutrient burn from occurring when growing marijuana plants.

  • Always follow the directions as indicated on the nutrient product of your choice. Never add more per milliliter of water than is recommended, and never provide your plants with nutrients more often than is recommended. We recommend looking up a nutrient schedule for your marijuana plants.
  • Also remember that new potting soil generally has plenty of nutrients in it. Therefore, when you first plant new marijuana plants, you really don’t need to provide them with any nutrients for anywhere from two to four weeks. The nutrients present in the soil combined with the nutrients that you add could definitely lead to nutrient burn.
  • If you see any signs of nutrient burn occurring, immediately stop providing your plants with more nutrients. If you see any signs, immediately start flushing them with water.

3. Magnesium/Calcium Deficiency


The other cause of rusty brown spots on your weed plant is if the plant in question has either magnesium or a calcium deficiency, or both.

Although a small magnesium or calcium deficiency is not the end of the world, it will just continue to get worse if you don’t address it.

This is especially the case as the plant moves onto the flowering stage, as it will require decent amounts of both nutrients in order to produce big and potent marijuana buds.

If you see those rusty brown spots on your leaves, especially large and blotchy spots, combined with leaves that begin to curl, it’s a sign that your plant is not getting enough calcium.

However, if the leaves form large brown spots, and also start to turn yellow, but the veins of the leaves stay green, then it is a sign that your plant is not getting enough magnesium.

Generally speaking, a calcium and magnesium deficiency results in leaves that have large yellow spots, with a good deal of brown spots as well, and more often than not, those leaves will begin to curl.

This generally starts happening on the newest leaves that grow, but as the deficiency continues, the middle aged leaves, and then the oldest of the leaves will also begin to exhibit symptoms.

Other signs of calcium and magnesium deficiencies in marijuana plants include dead spots on the leaves, crinkling or curling of the leaves, small or distorted leaves, stunted growth, curled leaf tips, and very dark green spots around the affected yellow and brown spots.

What Causes Magnesium/Calcium Deficiency?

There are two main causes of a magnesium and/or calcium deficiency in your marijuana plants. The first is quite simply that you haven’t been giving your plants enough nutrients.

Yes, there are many nutrient products and fertilizers out there, but not all of them contain magnesium and calcium. Of course, phosphorus, potassium, and nitrogen are the three main nutrients that plants need, but micronutrients such as calcium and magnesium are important too.

Your plant might just not be getting enough of those nutrients due to inadequate fertilizer. The second cause of magnesium or calcium deficiency is if your plant is suffering from so called nutrient lockout.

Nutrient lockout occurs when the roots are no longer able to properly absorb nutrients from the soil and the water. This generally happens because the plant is being kept in soil and water conditions that do not feature the right pH level.

For the record, the pH level is how acidic the soil is. If soil is either too acidic or too basic, which also applies to the water and nutrients that you are feeding your plants, then the roots will no longer be able to absorb the nutrients, and therefore lead to a nutrient deficiency.

Keep in mind that this nutrient deficiency doesn’t just apply to calcium and magnesium, but to all nutrients in general. Therefore, keeping your plants in the proper pH levels is important when it comes to them being able to absorb nutrients.

There are also some other minor causes here besides pH level. One thing that may cause nutrient lockout to occur is if the soil is far too wet. If the soil is too wet, eventually the roots will start to rot and will no longer be able to absorb nutrients.

Moreover, if the growing conditions are far too cold, this nutrient lockout can also occur. Plants just can’t function properly if they are too cold.

The other possible cause here is if the ratio of the minerals that your plants are getting is not proper. If the balance between potassium, ammonia, calcium, and magnesium is not right, it can also lead to your plant not being able to absorb nutrients.

How To Treat Magnesium/Calcium Deficiency

In order to treat a magnesium or calcium deficiency in your plant, the first thing you want to do is to check the pH level of the soil. The pH level of the soil should be between 6.8 and 7.2.

If the pH level of the soil is not between 6.8 and 7.2, you need to take the appropriate steps to treat it. Generally speaking, this means getting pH altering liquids, such as pH up and pH down, which are then added to your water, which will then in turn alter the pH level of the soil.

For instance, if your pH level is 7.5, you are going to want to add some pH down in order to decrease the pH level. Moreover, you also want to have a pH tester or pH meter, so you can test both the soil and the water for pH levels.

Of course, if your soil has an extremely low pH level, it’s going to take quite a high pH level in the water to balance things out. The trick here is of course to find a good balance.

Moreover, if you see that the soil is way too wet, almost soaking wet, then you just need to stop watering your plants for a while to give those roots a chance to dry out.

Do keep in mind that if the roots are way too far along and are completely rotten, there is likely no saving your weed plant. If the issue is that the air is far too cold, then the simple solution is of course to increase the air temperature to the proper level.

If none of these issues are the cause of the magnesium and calcium deficiency, then the only other reasonable explanation is that you simply aren’t providing your plants with enough of these minerals.

Therefore, go get yourself a nutrient product that contains ample amounts of both magnesium and calcium. Just keep in mind not to overdo it, because you can easily cause nutrient burn to occur.

All you can do is add the proper amounts of nutrients to your plants. However, adding excess amounts of nutrients to make up for previous deficiencies is not the way to go.

You need to solve the nutrient deficiency without causing nutrient burn.

How To Prevent Magnesium/Calcium Deficiency

  • The best way to prevent a magnesium or calcium deficiency from occurring is to simply provide your plants with enough of these nutrients in the first place. Go out and buy a good fertilizer or liquid nutrient product that contains ample amounts of both.
  • Ensuring that your plant is growing in the proper temperatures and does not get overwatered will help prevent nutrient lockout from occurring, and therefore nutrient deficiencies.
  • Ensuring that the soil in which your plant grows, as well as the water you give your plant, has a pH level between 6.8 and 7.2 will also help prevent calcium and magnesium deficiencies.

Do Rust Spots Only Appear During The Flowering Stage?

Although rust spots appearing on your marijuana plant leaves does most commonly occur during the flowering stage, it is something that can occur during all growth stages.

Cannabis Rust Spots On Leaves During Veg

Yes, marijuana plants require more magnesium and calcium when they are flowering than during the vegetation stage, so a nutrient deficiency is more likely to occur during the flowering stage.

However, if the pH level of the soil is not correct, if the air is too cold, or if the soil is too wet for too long, then a nutrient deficiency can occur at all growth stages. Moreover, nutrient burn can also occur at all growth stages.

This is especially the case for new plants that are planted in brand new potting soil that is loaded with nutrients, with growers then adding more of their own nutrients.

The result is that small and young plants are flooded with nutrients that will quickly burn them. Also, although rust fungus most commonly takes hold in flowering weed plants, it can definitely also affect plants in the vegetative state.

Rust Spots On Cannabis Leaves: Conclusion

As you can see, in most cases, brown rust spots on weed leaves are fairly easy to take care of. A nutrient deficiency is easy to solve, rust fungus isn’t much worse, and nutrient burn is the only issue that can cause serious and long lasting damage.

The trick is of course to identify and diagnose the underlying cause and to provide treatment as fast as possible.


My passion for the sticky icky started nearly a decade ago, and it all began when I first laid my eyes on the beauty that is the marijuana plant.

I cover all aspects of growing from equipment recommendations to plant health/care tips to help both new and experienced growers.