7 Tips to Prevent Rotting Seedlings from Damping Off

Do you struggle with rotting seeds after they've been planted? Damping off is a disease that can plague gardens of any size. In this article, gardening expert and former organic farmer Logan Hailey shares how to prevent this fungal disease that can destroy your seedlings this season.

seeds rotting


You worked so hard to sow all those seeds, and now they’re flopping over and dying before they get a chance to grow. If you notice young plants weakening at the base of their stem and never making it past the seedling stage, you’re likely dealing with a disease called damping off.

This aggressive fungus attacks emerging seedlings right at the soil surface. It can be detrimental to your seedlings, and it’s extremely important to prevent it from impacting your baby plants.

While you can’t cure damping off, you can easily prevent it with proper sanitation and environmental control. Improve your seed-starting success with these 7 simple ways to prevent damping off.

What is Damping Off?

Damping off is a plant disease that attacks young seedlings just before or after germination. The symptoms include rotten seeds, poor germination rates, seedlings with weakened stems, moldy or fluffy growth at the plant base, and baby plants that collapse shortly after emergence.

The disease is caused by pathogenic fungi and molds (namely Rhizoctonia, Fusarium, or Pythium) that thrive in overly wet, cold conditions where there isn’t enough aeration. Damping off is not curable, but it is easily preventable.

Can a Plant Recover From Damping Off?

Top view, close-up of seeds in a tray with a wet soil mixture, affected by a fungal disease - damping off. Seeds are oval and brown with small white sprouts. The soil is covered with white mold.
Once your seeds are infected they cannot be cured.

Damping off kills seedlings shortly before or after emergence. Once a seedling falls victim to damping off, it’s done for. You will need to throw it out, sanitize the environment, and restart.

You cannot cure damping off disease, but you can easily prevent it. Plant seeds in a well-drained soil mix, sterilize your seed-starting pots, provide plenty of airflow, prevent overcrowding, and avoid overwatering.

Key Takeaway: You cannot cure damping off, and you actually don’t want to. It is much smarter to re-seed so that your plants are robust and healthy. This disease severely weakens a baby plant’s stem, making it struggle to survive. Even if you can keep a dampened-off seed alive for a while, the plant will be severely stunted and prone to a range of other problems down the line.

Causes of Damping Off in Seeds

Close-up of melon seedlings in seed-growing trays. One of the seedlings is infected with damping off, it is sluggish, rotting, with white mold at the base of the stem. The seedlings have short, pale green stems and a pair of oval, slightly hairy leaves. The soil is wet.
The main causes are damp, poorly drained soil and poor airflow.

Cold, moist soil and weak plant growth are usually the reason your seedlings are falling victim to damping off disease. This disease is caused by pathogenic fungi and water molds that thrive in excessively moist conditions.

While these organisms can live in the soil without causing any problems, they become an issue when you create an environment that welcomes them. The key causes include the following:

Poor Drainage

A poorly drained soil medium is the number one cause. As water pools on the soil surface or sits stagnantly in heavy soil, seeds begin to rot. You may notice slimy, green growth on the soil surface.


Excessive water is like a shiny invitation for fungus and mold. Seedlings need to stay consistently moist but never saturated. You may notice mushy, tan spots on seedlings that are overwatered. Alternatively, seeds may not germinate at all because they rotted in soggy soil. Overwatering and poor soil drainage go hand-in-hand.


Soil temperatures below 65°F create conditions where damping-off pathogens can easily multiply. Research shows that the pathogens are suppressed by heated germination mats that keep container soil temperatures above 70°·F.


If you plant too many seeds in a small space, they will become more prone to diseases. Overcrowding can cause issues both in seed trays and out in the garden. The lack of airflow between seedlings weakens all of the plants and creates stagnant conditions where mold can grow.

Improper Composting

Compost is an amazing asset for any garden, but if you are making your own compost, you have to be sure that the pile reaches proper temperatures. The ideal mix of nitrogenous and carbon-rich materials allows compost to naturally “cook” out pathogens.

Studies show that one mold that causes damping off (Pythium sp.) is suppressed when composts are allowed to heat above 140°F and use hardwood tree bark. If you don’t have the time or energy for a proper composting process, it’s best to utilize a sterile seed mix.


This fungal infection is easily spread by unsanitized seed trays, contaminated potting mix, and unclean tools. It’s important to sanitize all seed-starting equipment using a diluted bleach solution. Avoid re-using potting mix or soil from your garden when you’re starting new seeds.

7 Ways to Prevent Damping Off

Damping off can be an aggressive disease that kills off loads of seedlings. Fortunately, it can also be quickly eliminated by a few cheap environmental adjustments.

You don’t need to treat seeds with fungicides or spray any harmful chemicals. Instead, use these cultural practices to keep pathogens away from your seed-starting trays.

*Please note that damping-off an happen to both indoors and outdoor seeds. These recommendations are primarily for gardeners who start seeds indoors in a greenhouse, windowsill, or nursery. However, you can apply the same principles to directly-seeded crops in the garden.

Use a Quality Seed-starting Mix

Plastic trays for planting seeds filled with fertile, well-drained soil. Spoon with soil over the trays. Trays are plastic, black with deep square cells.
Make sure the potting mix has good aeration and drainage to prevent stagnant and damp conditions in which fungi thrive.

Even the strongest seeds in the world cannot thrive in poor soil. Damping off begins in the soil, which means you need to select the most well-drained seed starting mix possible. The vast majority of seed-starting issues can be solved right at the source by simply changing the planting medium.

Proper drainage ensures that water flows seamlessly through the soil profile and doesn’t get “clogged up” in any part of a seed tray. The result is a well-moistened seed that is never sitting in water.

Key Takeaway: Aeration and drainage prevent the stagnant, damp conditions that fungi like to hang out in. If a seed-starting blend drains water quickly, the pathogens are less likely to attack your seeds.

Check that your seedling mix has enough drainage by doing this drainage test:

Drainage Test Steps

    • Fill a seed tray or pot to the top with the mix.
    • Avoid pressing or tamping it down.
    • Hold a hose or watering can over the seed tray.
    • Saturate the container.
    • As the water hits the soil, notice what it does.
    • If the water pools up on the top or runs off  the side, this indicates that the soil isn’t draining fast enough.
    • If the water immediately penetrates the soil surface and quickly drains out of the bottom hole (within 20-30 seconds), this a sign of adequate drainage.

It’s also important to remember that potting mix is not the same as a seed-starting mix. You don’t want to use just any old soil to start seeds. Ensure the best conditions possible by choosing a well-drained seed-starting mix. Most store-bought seedling mixes are already sterilized and formulated for ideal drainage.

Don’t Compact Your Soil

Top view, close-up of a male hand loosening the soil in seed starter trays with a small garden rake. The tray is large, black, plastic, and has square deep cells filled with soil. There are also a paper bag with soil and a spatula, and three bowls with various seeds on the table.
Use well-drained soil and avoid compaction.

Healthy seeds need to breathe just like we do! Whether you are planting in a seed tray or out in your garden, it’s important that seedlings can “breathe” in the soil they’re planted in.

When soil is compacted, it means there aren’t enough air spaces or holes for water and oxygen to pass through. These compacted zones are considered hypoxic, which means there is little to no oxygen. The lack of oxygen weakens the plant’s vigor and predisposes it to disease problems.

A seed sitting in compacted soil is more likely to fall victim to this fungal disease because pathogens love low-oxygen conditions. Moreover, compacted soil cannot properly drain water.

Imagine a dense stack of books versus a stack of bowling balls. If you pour water over the books, it will take a long time for the water to soak through all the little papers between the covers.

But if you pour water over a stack of bowling balls, there are lots of air spaces and holes where the water can go, which allows the bowling balls to become evenly moistened.

The stack of books is like compacted heavy clay soil. The stack of bowling balls is like well-drained, uncompacted soil. To prevent damping off, we want to create the latter conditions.

How to Prevent Compaction

  • Never press down or force the seedling mix into a cell tray.
  • Fill the tray, tap it on a table to let the mix settle.
  • Then add a small amount of mix on top.
  • You should not tamper down the mix.
  • Avoid seeding into compacted soil (especially heavy clay) in your garden.
  • If direct seeding, add aeration with a broad fork and amendments.
  • This will improve drainage.
  • Use amendments such as vermiculite, fine compost, or peat moss.
  • For outdoor seed beds, avoid excessive tilling that destroys soil structure.

Key Takeaway: Compaction removes oxygen from the root zone of a seedling. The damping off disease loves low-oxygen zones. Prevent the disease by ensuring plenty of aeration.

Avoid Overwatering

Close-up of watering tomato seedlings in a black tray with a green watering can. Tomato seedlings are small, have very thin white-pink stems with a pair of oblong oval leaves of pale green color.
Damping off can occur due to excessive watering.

Seeds need plenty of water to germinate and thrive in their early stages. However, some gardeners give their seeds a little bit too much water. We all know that fungi and mold love moist spaces. If the soil is over-saturated, damping off is more likely to occur.

Signs of Overwatering

  • Green slime, algae, or mold growing on the soil surface
  • Seedlings look wilted, yellow, or weak
  • Young leaves fall off
  • Slow, stunted growth
  • Soaked spots or blisters on stems and leaves
  • A foul smell from the soil
  • Extremely dark-colored soil mix

When seeding indoors, overwatering is easy to prevent. You need to create a watering schedule that is catered to the seedlings rather than your clock. Irrigation does not occur in a set time frame; it depends on temperature, humidity, drainage, and the size of a container.

Check your seedlings once per day. When its time to irrigate your seedlings, remember to:

  • Only water until soil flows out of the bottom drainage hole, then stop.
  • Always check the soil moisture before watering.
  • Put your finger in the tray and observe the texture.
  • If it looks like a brownie mix and sticks to your skin, it is probably too saturated.
  • If a little bit sticks to your skin but the mix still looks crumbly, it is a great time to water.
  • If the mix feels bone dry and doesn’t stick to your skin at all, the seeds need water immediately.
  • Balance is key: You should never let seeds dry out!

Of course, you cannot control excess rainfall out in the garden. If you are having problems with damping off in your outdoor soil beds, consider installing a low plastic tunnel over the seeds and watering them with drip irrigation.

Key Takeaway: Healthing seedlings require consistently moist soil that is never soggy. Too much water can cause rotting and damping off.

Thin Your Seedlings

Close-up of female hands with scissors thinning out young pea seedlings in a plastic tray on a table covered with burlap. The seedlings are small, with slender, pale green stems and a pair of glossy, heart-shaped, pale green leaves.
Thin out your seedlings to avoid overcrowding and ensure proper airflow.

Nobody enjoys being packed in a subway like sardines. We all need our personal space, and seedlings are no different. Overcrowded plants are prone to a wide range of problems, including damping off.

Again, this comes down to airflow. Seeds that are growing super close together will have stagnant air and excess moisture near the soil surface.

In addition, overcrowded seedlings will compete with each other for light, water, and nutrients.

Thinning may feel like it’s reducing your yields, but it’s actually allowing your plants to grow stronger and healthier. It’s OK to sow extra seeds to ensure you get enough germinated plants. However, if you forget to thin them, you risk losing your harvest chances.

Thinning depends on the recommended crop spacing and growth conditions. Check your seed packets and use these rules of thumb to guide you:

Seed Thinning Steps

  • Thin seedlings after germination when they have reached 1-3” tall.
  • Get ‘em while they’re young so your plants have the best chance of survival!
  • Choose the strongest, tallest seedling and remove the rest.
  • Use tiny scissors or needle-nose pruners to cut seedlings at the base.
  • Yanking them out can disturb the roots of the plant you want to keep.
  • When growing in seed starter trays, thin to just 1-2 seeds per cell.
  • Multiple plants in a small cell can cause stunting and disease problems down the line.
  • When seeding in your garden beds, thin based on the crop variety recommendations and the size at which you want to harvest the plant.
  • For example, if you enjoy tender baby radishes that are about 2” in diameter, thin your radish seedlings to 2-3” between plants.

Key Takeaway: Overcrowding causes stagnant air and excess moisture to accumulate at the base of seedlings. Un-thinned seedlings create a breeding ground for fungi and mold.

Provide Plenty of Airflow

Black fan in the greenhouse against the background of blooming pink and white tulips. Round fan with black blades and protective grille. Tulips have cupped flowers with upright pink and white petals, and dark green oval leaves with pointed tips.
Use a fan to simulate natural airflow and prevent this fungal disease.

Sometimes a fan is all you need to get rid of damping off. Fans are among the most underrated gardening tools. If you are starting seeds in your home or a greenhouse, a fan mimics the natural breeze and prevents stagnant air near the seedling root zones. Remember that pathogens love hypoxic (low oxygen) zones.

Place a fan 2-4 feet away from your seedlings to ensure adequate air movement. Air circulation from an angle slightly above the seed trays is ideal. This will keep the soil surface dryer so that mold doesn’t grow at the base of young plants.

The fan should not be excessively strong, but it can very slightly blow the seedlings like a nice, pleasant breeze. Size your fan according to your space and avoid fans that are too powerful.

If you cannot add a fan, be sure that air can flow through the seed-starting space. For some, this may require rolling up the sides of greenhouses or low tunnels during the day.

Sterilize Containers and Tools

Close-up of seed sowing trays with plastic lids covered with condensation. Trays are sterilized.
Be sure to wash and sterilize seed trays and garden tools well to prevent fungus infestation.

Like many plant diseases, the fungi that cause damping off can hitchhike between plants via containers and tools. Sterilization is a major issue on commercial farms and nursery operations, but it isn’t as big of a deal in a small garden. Nonetheless, it’s an extra layer of protection.

There is nothing wrong with reusing your garden containers. After all, it’s eco-friendlier and more affordable. However, it’s essential to sanitize trays before you use them.

If you’ve had previous problems with damping off, take an extra 5 minutes before planting to sterilize the area. You can use a solution of 10% household bleach (or a capful in a spray bottle of water) and drench the container surface.

Additional sterilization practices include:

  • Source sterile seed starter mix.
  • Wash all garden tools.
  • Wear gloves when filling seed trays.
  • Wash hands after handling infected plants.

Key Takeaway: Keep a handy spray bottle with diluted household bleach to sanitize all trays and tools before and after each use.

Throw Away Infected Plants

Close-up of infected young seedlings in seed trays. Cabbage seedlings have sluggish, pale green stems and round, slightly serrated leaves. Some leaves are dry, with brown spots.
If your seedlings are affected by a fungal disease and cannot recover, discard them and start over.

Prevention sometimes involves a brutal cull. The most important final step to get rid of damping off is accepting that your seedlings can’t recover. Throw them out!

If your seedlings show any of these signs, get rid of them ASAP and restart.

Seedling Infection Symptoms

  • Collapsed young plants.
  • The base of the stem looks like a thin thread.
  • The base of the stem has yellow or brown spots.
  • Watersoaked lesions on the plants.
  • Moldy or fungal-looking growth near the soil surface.

Put those babies in the trash, and do not reuse the soil mix! Get a fresh start with new seeds that can grow into strong, resilient plants!

Final Thoughts

Ultimately, stagnant air or water are the core causes of damping off. You can easily prevent this seedling disease by:

  • Using a well-drained seedling mix.
  • Preventing compaction.
  • Avoiding excess irrigation.
  • Thinning your seedlings.
  • Ensuring plenty of airflow between plants.
  • Sanitizing your tools.

By making sure you stick to the following tips, you’ll be well on your way to providing your seedlings their best chance at survival. While you cannot treat damping off, you can certainly do your best to prevent it by following the guidance given above.

Gardener is direct seeding seeds into the ground on the left, and sowing indoors into trays on the right.


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