Skip to Content

Get Rid of Soil Fungus In Your Garden: Identification & Treatment Guide

Get Rid of Soil Fungus In Your Garden: Identification & Treatment Guide

It is crucial for gardeners to identify and manage fungi found in garden soil, as while many are beneficial for plant health, some can cause diseases. If any challenges prevent you from rewriting this, please reply with the error message: Unable to process the request due to encountered difficulties.

To identify the detrimental fungus in the garden, look for signs of plant stress such as wilting or discoloration. Treating these fungi effectively can involve using appropriate fungicides or enhancing the presence of beneficial fungi to naturally suppress harmful varieties.

This guide goes beyond identification and treatment, exploring causes and preventive measures for garden soil fungi. It offers practical, science-backed advice for maintaining a healthy garden ecosystem.

Key Takeaways

  • Identification of Harmful Garden Fungus: Look for plant stress signs like wilting or discoloration. Beneficial fungi appear as white, thread-like networks, while harmful ones show as discolored, fluffy growths.
  • Prevention: Ensure well-aerated, nutrient-rich soil and avoid overwatering. Use mulch carefully and maintain regular garden monitoring.
  • Treatment: Remove infected plants, improve soil drainage, and use appropriate fungicides. Consider natural treatments like baking soda solutions as an organic alternative for mild fungal issues.
How to identify fungus on plants and what to look for

Garden Fungus Identification – What to Look For?

Identifying fungus in garden soil and fungus on plants is crucial for maintaining plant health. While some fungi play a beneficial role, others, like those causing root rot, can be harmful. Me sure to skim our article on healthy soil inoculants as you work through this info, to plan how to keep your soil healthy. Here’s a straightforward guide to help you differentiate them:

  • Observe the Appearance: Beneficial fungi often form mycorrhizal relationships with plant roots, enhancing nutrient absorption. These fungi usually appear as white, thread-like networks.
    In contrast, harmful fungi, such as those causing root rot, often manifest as discolored patches or fluffy growths on plant roots and soil.
  • Check Plant Health: Plants affected by harmful fungi will show signs of distress, like wilting, yellowing, or stunted growth. If your plants are thriving, the fungi present may be beneficial.
  • Monitor Soil Conditions: Beneficial fungi thrive in well-aerated, nutrient-rich soil.
    Harmful fungi are often prevalent in overwatered or poorly drained soils.
  • Consult an Expert: If you’re not sure about the type of fungus, it’s advisable to seek advice from a gardening expert or a plant pathologist.

A beneficial plant fungus typically appears as a white, thread-like network around roots, enhancing growth, whereas harmful fungi often manifest as discolored, fluffy growths on plants, indicating damage

How to treat garden fungus infection?

How to Get Rid of Fungus in Garden – 10 Steps

Follow these 10 easy steps to effectively get rid of the fungus in your garden soil:

  1. Identify the Fungus: Conduct a soil test to identify the type of fungus. Understanding whether it’s beneficial mycelium or harmful is crucial.
  2. Remove Infected Plants: Often, fungus spreads through infected plants. Remove and dispose of them safely to prevent further contamination.
  3. Improve Soil Drainage: Ensure good drainage in your garden. Waterlogged soil is a breeding ground for harmful fungi.
  4. Use Fungicides Wisely: Apply a top-notch, appropriate fungicide. Be specific in your choice; some target only certain types of fungi. (Source)
  5. Introduce Beneficial Nematodes: These microorganisms can help control certain fungal infections by breaking down the harmful fungi’s network. (Source)
  6. Adjust Watering Habits: Overwatering encourages fungal growth. Water plants only when necessary.
  7. Sterilize Garden Tools: Always sterilize your garden tools after use to prevent the spread of the fungus.
  8. Apply Organic Matter: Mix well-composted organic matter into the soil. This can improve soil health and suppress harmful fungi.
  9. Use Mulch Carefully: While mulch can retain moisture, ensure it’s not too thick as it can harbor fungus.
  10. Regular Monitoring: Keep an eye on your garden for signs of fungal reoccurrence. Early detection is key to control.

Indoor Plant Fungus

Leaf Spot

You will notice yellow or brown spots on the leaves. Take off these leaves right away. If the problem persists, further treatment is needed.  

Root and Stem Rot 

The plant might wilt slowly over months. Its leaves will become dull, yellow, and limp.

Botrytis (AKA Bacterial Soft Rot)

Bacterial Soft Rot On Young Pepper Plant

This parasitic fungus tends to attack fruits and young saplings. First, you will notice a part of your plant going brown, followed by a fuzzy brown growth. 

Powdery mildew 

Powdery Mildew On Flower Bud

You’ll see a white dust-like substance on leaves, often starting underneath. Check plants often to prevent them from spreading.

Garden Fungus  

Garden plants can also have problems with the fungi I mentioned above. But here are a few more species that tend to attack outdoor plants. 


Anthracnose On Grape Leaf

Black marks will appear on leaves, especially on fruit trees. They look bad but are not very harmful.


Blight On Tomatoes and Stems

Brown spots will appear on plants or dark patches on flowers. Blight gets worse with grey fuzzy mold.


Rust On Oat Plant Stem

You’ll notice round, orange-brown blisters on plant stems. These are a big problem for cereal plants.


Swollen Roots from Clubroot

Underground, clubroot is easy to spot. The roots look changed and swollen.

But if you don’t want to rip your plant up to check what’s wrong with it, look out for more subtle signs like wilting. (Even if you’re watering your plant enough, the damaged roots won’t be using water effectively.)

What Causes Soil Fungi?

Fungus is naturally in the soil. Its spores can sleep in the earth for hundreds or thousands of years. Then, when conditions are right, they will ‘wake up’ again. But what causes it?

  1. Too Much Moisture In The Soil: Avoid overwatering plants. Aim your hose or watering can at the plant base to keep leaves dry.
  2. An Unbalanced Soil Community: Maintain a balance of bacteria and fungi in your soil. Pathogenic fungi thrive in unbalanced soil conditions often caused by pesticides or tilling. Opt for organic, no-dig methods.
  3. Lack of Oxygen In The Soil: Ensure your soil has adequate oxygen. Prevent soil compaction by avoiding heavy machinery and using cover crops. Note that rototillers may worsen compaction below the surface layer. If your soil doesn’t have enough oxygen, it becomes a breeding ground for pathogenic fungi and bacteria. This means the beneficial organisms can’t compete with the harmful kinds, and the pathogens will take over. 
  4. Unhealthy Potting Soil: Even with proper care, contaminated potting soil can introduce fungi. Choose a reputable compost source and consider experimenting with different types. Get your potting soil from a trusted source, and don’t use old potting soil from last season if it’s been sitting out. And remember: compost isn’t a replacement for soil.

How to do a Soil Test?

Soil Being Tested In A Lab

It’s possible, and even routine, to test soil for fungus. For me, regularly testing my soil is one of the most important parts of gardening. There are test kits that you can do at home, but you’d be better off contacting your local council and asking them if they have an affordable soil testing program while keeping these details in mind:

  • Routine Testing: Regular soil testing is crucial for effective gardening.
  • Home Kits vs. Professional Testing: Home test kits lack reliability. Opt for services offered by local councils or reputable soil technicians.
  • Sending Samples: Ensure samples are sent in aerobic conditions (e.g., a plastic bottle with air space) to avoid false indications of unhealthy soil.
  • Importance of Aerobic Conditions: Avoid small, airtight containers. They can create conditions favoring harmful fungi, leading to misleading results.
  • Compost Testing: Test your compost or source it from operations knowledgeable about soil microorganisms. Note that municipal compost is often sterile and can encourage pathogenic spores if devoid of beneficial bacteria and fungi.

How Do You Get Rid Of Fungus In Soil?

Preventative measures are key in dealing with garden fungus. Relying solely on fungicides leads to a cycle of eliminating both harmful and beneficial soil organisms. Beneficial fungi are crucial for a healthy garden, but if you notice white fuzziness or signs of harmful fungi on plants, action is necessary. This section emphasizes the importance of balance and careful response to fungal issues in gardening.

Here are some ways that you can get rid of fungus:

  1. Prune Diseased Leaves: Remove affected leaves and prune healthy ones for better air circulation. Avoid removing more than 30% to maintain photosynthesis.
  2. Improve Conditions: Address root causes like waterlogged soil, inadequate air circulation, or overwatering. Rotate crops and focus on soil health with quality compost.
  3. Use Fungicides Cautiously: Fungicides can be useful, but they treat symptoms, not causes. Opt for safe options and investigate underlying issues.
  4. Address Soil Health: Regularly apply quality compost, reduce fungicide use, and check for soil compaction to prevent future problems.

Will Baking Soda Kill Fungus In Soil?

Baking soda will kill fungus in the soil in large enough amounts, but it’s best used as a foliar spray. Nevertheless, this is a good solution for somebody with an occasional problem with fungi. 
I recommend using baking soda because it doesn’t have the same health or wildlife implications that chemical fungicides can pose.

Using Baking Soda On Plant Fungus 

  1. You can fill a spray bottle with water
  2. Mix in a few drops of vegetable oil
  3. Add a teaspoon of baking soda
  4. Mix the solution very well
  5. Spray topically on plants 

After you’ve dealt with the fungus on the leaves, you would ideally respray the plant with a compost tea. This will replace the good bacteria and fungi that you just killed along with the pathogen and prevent the problem from reoccurring. 

You could also sprinkle baking soda on areas of the soil where you can see fungus. But it will also kill the beneficial organisms. A better solution would be to dig any fungal areas out of the soil, break them up and sprinkle them over your compost heap. 

The breaking, sunlight, and oxygen should kill it off without the need for baking soda. 

Does Boiling Water Kill Fungus In Soil?

Boiling water can sterilize soil by killing fungus, making it suitable for potting. However, this process also depletes essential nutrients. Using fertilizers to replenish these nutrients might inadvertently encourage fungal growth. Managing soil fungus effectively requires a balance and understanding of nature. This process can be complex but becomes more manageable with experience. Focus on gradual learning and adapting your approach to soil care.

Will Vinegar Kill Garden Fungus?

While vinegar can kill garden fungus, it might also harm weakened plants.
Using vinegar in gardens is not generally recommended, especially for plants already struggling with fungi. However, if the choice is between vinegar and chemical fungicides, vinegar is preferable due to its lower cost and fewer health risks associated with inorganic chemicals.


  1. Can fungi be a cause of lung infections? Yes, soil fungi like Histoplasma, Coccidioides, and Blastomyces can cause lung infections when inhaled, particularly in individuals with weakened immune systems. (Washington University School of Medicine)
  2. What are the common types of garden soil fungi? Common types of soil fungi in an outdoor garden include beneficial mycorrhizal fungi, aiding plant growth, harmful fungi like Phytophthora causing root rot, Rhizoctonia known for root and stem rots, Powdery Mildew affecting leaves and stems, Sclerotinia causing wilt and rot, as well as other varieties like slime molds, stinkhorns, and bird’s nest fungi. Each of these has unique characteristics and impacts on garden health
  3. What fungicides should be avoided on houseplants? Avoid harsh chemical fungicides, especially copper-based ones, for houseplants. Opt for milder, organic options like neem oil or sulfur-based products.
  4. Can garden fungi affect household plants? Yes, fungi like mold and mildew can affect household plants, particularly in damp conditions. Proper watering and good air circulation are key preventive measures.