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How To Get Rid Of Mold Growth On Germinating Seeds, Seedlings & Seed Starter Pots

Finding mold on seedlings is frustrating! In this post, I’ll show you step-by-step how to get rid of mold growing on your germinating seeds, starts, soil, and pots, and prevent it from coming back.

When mold starts growing on your carefully cultivated seedlings, it can be very disheartening.

It’s definitely one of the most annoying things about caring for seedlings, and something I get asked about a lot. But the good news is that it’s easy to fix!

Unfortunately, mold growth on seedlings, inside of seed starter trays, or on the pots can be a common problem. No matter what your experience level, you’re sure to run into this at some point.

The best thing you can do is to catch it early, and take steps to prevent it from growing in the first place. Keep reading to learn how to get rid of mold on your germinating seeds and new growth starts.

Here’s what you’ll find in this step by step guide…

Table of Contents

Why Are My Seedlings Molding?

We all know that mold thrives in a warm, damp environment. Well, those are the exact conditions that many seeds like to sprout in!

So, if we’re not careful, our seed trays can become the perfect breeding ground for all kinds of mold and mildew: white and fuzzy, green, yellow, or orange.

It’s scary to discover you have moldy seedlings for the first time! But don’t worry, it’s a problem that’s easy to fix with a few small changes.

Seedlings in covered trays are prone to mold

Will Mold Hurt My Seedlings?

The good news is that the mold itself will not kill your seedlings. However, it is a sure sign that something else is wrong, and needs to be fixed ASAP.

Because what could eventually kill them is what causes the mold to grow in your seed trays in the first place.

The main causes are overwatering, improper ventilation, too much heat, and/or overcrowding. All of which I’ll talk about in detail below.

White fuzzy mold on seedling soil

How To Get Rid Of Mold On Seedlings

The good news is that it’s easy to get rid of the mold growing in your seedling trays, and you don’t need to buy any chemical sprays or powders. Simply follow these steps…

Step 1: Remove the mold – The first thing you should do is carefully scrape or pull it off the top of the soil. I know, this sounds like a really disgusting job, but it’s very effective.

I use a sharp pencil or a small knife to gently get as much of the mold off the soil as I can, and wipe it into a paper towel.

Don’t worry if you don’t get every single bit off the soil, or if you’re too squeamish to do this part. Once you follow the remaining steps, the rest of it will die off on its own. Scraping it off just helps to get rid of it faster.

Step 2: Ventilate your flats – If the lids are still on your trays or flats, this is definitely part of the problem.

I usually try to keep the lids on my trays until the seedlings get tall. But if mold starts to grow, then it’s time to ventilate them.

Use a pencil or other similar item to prop open one end of the lid to get some fresh air into your trays. If all of your seeds have germinated, then you can just remove the lid completely.

Ventilating trays to avoid mold on soil and seedlings

Step 3: Allow the soil to dry out a bit – It’s important to make sure you’re not overwatering. The soil should never be soggy, and any excess water should be dumped out after 30 minutes.

Ideally, try to keep soil evenly moist, allowing the top part to dry out slightly between waterings. Never let it dry out completely though.

Consistent overwatering not only causes mold growth, but it will eventually kill the seedlings. So always check it before watering to ensure you’re not giving them too much. An inexpensive moisture gauge really comes in hand here.

Step 4: Turn off the bottom heat – Once all of the seeds have germinated, it’s best to turn off the heat mat. Too much heat will encourage mold to grow, and can also harm your seedlings.

Mold growing on seedling pot

How To Stop Mold From Growing In Your Trays

Taking the steps above will get rid of existing the mold, but it can come back at any time.

To stop it from growing again, you need to maintain an environment where seedlings will thrive, but mold and mildew won’t.

It can be a bit of a balancing act, but you’ll get the hang of it in no time. Here’s how to it from coming back…

Air Circulation

Providing good airflow is the first defense. Keep an oscillating fan gently blowing and rotating over your trays during the day.

This airflow also has the added benefit of strengthening the tiny starts too. Keep a close eye on the moisture level though, because the fan will dry the soil out much faster.

Using a fan to prevent mold on seedlings

Water From The Bottom

Another great way to prevent mold growth is to water your seedlings from the bottom, rather than pouring it over the top.

Doing this makes it much easier to keep the top layer of soil dry, while ensuring the roots are getting enough moisture. Just make sure to pour out any water that hasn’t been soaked up after 30 minutes.

Watering seedling trays from bottom to prevent mold

Thin Them Out

Like I mentioned above, it’s very important that your flats get good airflow. Overcrowded seedlings can prevent proper circulation, which means the mold will likely grow back.

So, if yours are overcrowded, but too small to pot up, then you need to thin them out to give them plenty of room to grow.

Thin seedlings to allow proper airflow

Pot Them Up

If you don’t have the heart to thin them, pot them up instead. You can repot seedlings once they are twice as tall as the original container.

This makes it much easier to maintain proper soil moisture, and prevent future mold growth on your seedlings.

I like to use plantable pots to make transplanting everything a snap. But you can use plastic ones, if you prefer, or if you have problems with mold on biodegradable pots.

Potting up seedlings to prevent mildew growth

Add Lighting

Proper seedling lighting will also help prevent the regrowth of mold. Position a grow lamp so it always hangs a few inches above your starts, and give them 14-16 hours of light every day.

Plugging your fixture into an inexpensive outlet timer makes it easy. You can buy a grow light kit, or make your own DIY grow lights for seedlings.

How To Prevent Mold On Seedlings

Now that you know how to get rid of mold growing in your seed trays, let’s talk about how we can prevent this from happening in the first place.

Use The Right Soil

It’s extremely important to use the right type of soil in your seed trays. Regular potting soil is too heavy for seedlings, and can cause a whole bunch of problems (including mold growth).

Make sure to use a lightweight, and fast draining soilless medium that is specifically made for growing seeds. Or you can try to make your own mix.

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Disinfect Your Containers

Mold spores can lay dormant in dirty trays, and regrow year after year. So, it’s always a good idea to wash and disinfect your equipment between uses.

This is the best way to prevent any type of mold, mildew, or fungus, including seedling blight (which causes damping off), so don’t skip this step.

Use The Proper Equipment

If you’re just starting out, it’s so much easier to be successful when you use supplies and equipment that are specifically made for starting seeds.

I know this means spending a few extra dollars. But in the end, it’s worth the cost to avoid the frustration (and added expense) of losing all of your seedlings.

Finding mold growing on seedlings, the soil, or biodegradable pots and pods can be very scary and frustrating. It’s good to know that this problem is easily fixable by simply following the steps above.

If you need more help and guidance, you should take my online Seed Starting Course. It’s a self-paced, comprehensive online course that will walk you through step-by-step, show you exactly how to grow garden seeds, and care for your seedlings. Enroll and get started today!

Want to learn more about planting seeds indoors? Then pick up a copy of my Starting Seeds Indoors eBook. It’s a quick-start guide for beginners, or those anyone just looking for a refresher.

More Seedling Posts You Might Like

Share your tips for controlling and getting rid of mold on seedlings in the comments below.

About Amy Andrychowicz

I live and garden in Minneapolis, MN (zone 4b). My green thumb comes from my parents, and I’ve been gardening most of my life. I’m a passionate gardener who loves growing everything from vegetables, herbs, and flowers to succulents, tropicals, and houseplants – you name, I’ve grown it! Read More.

Comments

Great advice and I’ll be sure to follow next year! Currently, I have a dozen healthy looking seedlings in biodegradable pots that show white mold on the outsides. Is it okay to transplant the whole thing or should I try to gently remove the soil from the moldy containers before transplanting outside?

Amy Andrychowicz says

The mold growing on the biodegradable pots won’t hurt the seedlings once they are planted, so yes, you can just plant the whole pot outside.

Lacy Hooker says

Hi Amy,
At school we are growing seeds in jars with paper towel and they are getting mouldy. My friend and I have scraped the mould off but we don’t know what to do next. Do you have any suggestions?
Thanks,
Lacy and Mia

Amy Andrychowicz says

It’s very common for mold to start to grow when the seeds take too long to germinate using the paper towel method. The trick is to make sure you don’t overwet the paper towel (it should be wet but not completely soggy), and to make sure they are in a very warm place so they will germinate as quickly as possible. I would also try putting the paper towel into a zip top baggies rather than a jar, that will help them stay warmer and germinate faster so they won’t end up molding. Also, if they mold before they germinate, then it might mean that the seeds aren’t viable. Here’s an article with more details about how to successfully use the paper towel germination method. Good luck!

Lee Hernandez says

I have also tried sprinkling ground cinnamon over the top of the dirt after the seeds are down. It seems to work.

Amy Andrychowicz says

Great, thanks for sharing your experience for preventing mold growth in your seed trays! I’ll have to test using cinnamon next year.

Thank you. Bought some contaminated soil pods, and thought I may have to throw out that whole batch of starters, hopefully this will save them! None of the other brand soil pods are moldy, just the one tray. Of course it’s the expensive seeds in it…..

Amy Andrychowicz says

Haha, of course! Good luck getting rid of the mold.

Henry Wadds says

I have heard that mustard and cloves also prevent many fungi from multiplying but have not tried it myself

Shiela Hanlon says

Thanks for the great advice! I’m ventilating my seed tray now… will get in there shortly to scrape off the mold onto a paper towel. Glad I don’t have to trash my first effort at indoor seed starting.

Amy Andrychowicz says

You’re welcome, happy to help! Getting airflow in your seed trays should definitely help to get rid of that mold pretty quickly. Good luck!

If I have the trays in my home will the mold effect us?

Amy Andrychowicz says

Sorry, but I can’t say for sure. I would certainly recommend getting rid of the mold in your seed trays, because I can say for certain that it’s not good for your seedlings.

I am new to seed starting. I have found mold on the soil after a week of planting seeds. They smell very earthy when I lift the lud.
I am using peat pots and they absorbed all the water I put in the tray. I am using a grow light.
Not sure if peat pots are the problem.
Thank you for any advice.
Caroline

Amy Andrychowicz says

Peat pots certainly can mold, and it can be a problem. I would follow the instructions in this post to try to give them more ventilation, which will help prevent mold growth.

Sharon Poh says

Hi Amy, Thank you very much for the extremely detailed and useful information. There were several times when my herb seedlings got mold on them. And I threw them away. I should have searched for this information earlier. Now I know what to do.

Thanks again and good day!
Sharon

Amy Andrychowicz says

You’re welcome, glad I could help!

Before scraping off the soil, especially if the seedlings are nearing potting up size, I’ll use hydrogen peroxide sprayed directly on the seedlings and planting material. Then I’ll turn the oscillating fan up a notch (it runs 24 hrs/day) and watch my watering. Works for me. Only after that fails will I srart scraping the soil…

Amy Andrychowicz says

Great tip, thanks for sharing how you’ve successfully been able to get rid of the mold on the soil in your seedling trays. Sounds like you’ve got a good technique.

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Seeds crack, then rot (soft white stuff inside shell)?

Have you tried the paper towel method ? Wring out a paper towel so it’s not dripping, put seeds in it, fold it over, put them in a ziplock bag. I always blow into the bag, but that may or may not be a good idea and isn’t necessary just part of my tradition. Anyway seal the bag up with some air in it and then check on it every 12 hours or so refreshing the air and spraying with a TINY burst of water IT the paper towel is getting dry. Unfold and check for sprouting seeds and VERY carefully pull them off the paper towel. In same cases the tap root will have grow through the paper towel (which is probably the main disadvantage of this method) and you will need to tear away a little paper towel or just be extra careful and the tap root will pull away from the paper towel. You could use scissors to cut away some paper towel as well as having some paper towel on the tap root won’t hurt. Then drop them in soil or rockwool or coco or whatever you are using.

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Then I put the bag someplace dark and not cold. A desk draw should work. I’ve seen people stuff the bag under a cushion and get decent enough germ rates. On top of something mildly warm like a refigerator is ok, but you don’t want to take a chance with too much heat as that will kill them and room temp is good enough germ.

I supposed it could be your seeds suck too, but it’s probably your seedlings not getting enough air because your medium is too wet.

beefyomelette

jiffy peat pellets

jiffy peat pellets

thanks, i thought i should mention this is happening with jiffy peat pellets.

aasin527
Active member

that white stuff would be the seeds endosperm. the seeds food supply. so lets figure out why your seeds won’t complete germination. if you are using peat pellets resist the urge to pull the seed out to check on it. you are only damaging it. if you have any pics, that would be a good start. what variety are you growing? how old are the seeds? are you soaking them and then planting them?

RetroGrow
Active member
CANNATOPIA

Assuming you know what you are doing & knowing that most seeds pop right pretty easily with just a little moisture, I would place my bet on faulty beans.

Seeds not germinating and getting slimy?

slime is usually connected to temperature, so what are your ambiental and grow room conditions?

MynameStitch
Dr. Doolittle

I would not leave the seeds in water more than 24 hours; I would get a wet towel and place seeds in there and fold the flap down over the seeds. Slime would most likely be related to some kind of bacteria or fungus.

NiteTiger
Tiger, Tiger, burning bright.

I’ve had that happen before when germing seeds.

Adding a bit of H2O2 (hydrogen peroxide) to the water took care of it.

romdog11
Member
RottenDawg
Member

I’ve had that happen before when germing seeds.

Adding a bit of H2O2 (hydrogen peroxide) to the water took care of it.

HeadyPete
Take Five.

I’d have to agree with above, seed direct in substrate is my fave method. Closest to natural way.

Had 9/10 mountain jam pop like this, after 2 years in the fridge, 1 grew upside down and the peat pellet had to be opened and the seed and root turned around, but she is good today. Watch for difficulty of sprout shedding seed covering. If you do not release seedling from seed cover, it will die. Be gentle and slowly pick it off. A pin or needle is great for this. I think this is more likely the older the seeds are.

Peat pellet holes can be too deep and wide for seed so pack some worm casting or fine soil in the hole to the top, poke a new smaller hole, drop seeds and cover. Squeeze pellet slightly together to get good soil contact to seed, and make sure seed isn’t too deep. Just covered with 2 mm or so soil is best.

MynameStitch
Dr. Doolittle

have tried the paper towel method, but i hear once the root shoots you wanna put em in soil immediately instead of lettin em get long. and the papertowels dry out so you gotta watch em. how else do y’all germinate?

thanks for the help everybody.

Thats not true; as long as you keep the towel moist you are fine; I would use a container with a lid and holes to keep it moist inside and let them grow long tails to where the seed head was about to come off to show the cotyldons. But I always reccomend washing paper towels a lot because some companies still have junk left over that can cause the seed to not open.

Guest

I agree with my old friend stitch.

you should only soak the seeds for 12 hours.

just to hydrate them.

One big area I have with mandalamikes method is the transplant.

whats that about.

I use paper towel . wouldnt think of doing it any other way.

and let the roots get 1/2 to 3/4 long.

which prevents the root from growing upward .

MynameStitch
Dr. Doolittle
Hundredproof
Member

the mix i used (got from an ed rosenthal reference) is 1 part h202 (3%) to 5 parts water. he also said to mix in some rooting solution but i ommitted that part (why bother i figured).

just did it this last week as i lost 30 seeds to some kind of infection while germinating, all but one light green seed sprouted, ive now got 1 1/2 inch tall babies that are lookin great.

Hundredproof
Member

i guess that would work out to 3.2 cups of the 3% h202 to a gallon of water.

ed recommended a mix of 200:1 so if you have the stronger h202 youd need to rework it.

blAsia
Member

H2O2 is very “unstable” and dynamic. I never heard of 1 to 5 ratio with water.

Hydrogen Peroxide and Horticulture
By Bryce Fredrickson

Hydrogen Peroxide (H2O2) is a clear sharp smelling substance very similar in appearance to water (H2O). Like water it is made up of Hydrogen and Oxygen, however H2O2 has an extra Oxygen atom in an unstable arrangement. It is this extra atom that gives H2O2 its useful properties. H2O2 has been used for many purposes including cleaning, bleaching, sterilizing, rocket fuel, animal feed treatment and in addition many miraculous claims about its health benefits have been made. This article isn’t about any of these; instead it will concentrate on horticultural applications. H2O2 is of great use for both hydroponics and dirt/soilless gardening.

1. What Does Hydrogen Peroxide do?
H2O2 is an unstable molecule, when it breaks down a single oxygen atom and a molecule of water is released. This oxygen atom is extremely reactive and will attach itself to either another O- atom forming a stable Oxygen molecule or attack a nearby organic molecule. Both the stable and O- forms will increase the level of dissolved oxygen. This is the method by which H2O2 is beneficial. Pretreating the water supply with H2O2 will drive out the Chlorine many cities use to sterilize it. This will also degrade any pesticides or herbicides that might be present as well as any other organic matter. Well water can be high in methane and organic sulfates, both of which H2O2 will remove. Many disease causing organisms and spores are killed by Oxygen, the free Oxygen H2O2 releases is extremely effective at this. H2O2 will help eliminate existing infections and will help prevent future ones. It is also useful for suppressing algae growth. The free Oxygen atom will destroy dead organic material (i.e, leaves roots) in the system preventing them from rotting and spreading diseases.

2.Over Watering
Roots require Oxygen to breathe and low levels are the main cause of almost all root diseases. Both soil and hydroponic plants often fall prey to the same syndrome although it is rarely recognized as what it really is. Hydroponic crops often fail due to “root rot” and soil crops succumb to “over watering.” The real cause of both these problems is a shortage of Oxygen at the root zone. In a soil system the soil consists of particles, a film of water on the particles and air spaces between the particles. When too much water is put into the soil the air spaces fill with liquid. The roots will quickly use up what Oxygen is dissolved in the water, if they haven’t drunk enough of the liquid to allow air back in to the soil spaces they will stop working. In this situation roots will start dying within twenty-four hours. As the roots die the plants ability to drink water and nutrients will decrease, this will cause symptoms of nutrient deficiencies (mostly pale, slow, weak growth), and strangely they will start to wilt like they don’t have enough water. It is easy to make a fatal mistake at this point and add more water.

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In a Hydroponic system the cause is a more direct simple lack of oxygen in the solution, this may be from inadequate circulation and/or aeration. High reservoir temperatures also interfere with Oxygen’s ability to dissolve in the water. Temperatures above 70F (20C) will eventually cause problems, 62F-65F (16C-18C) is recommended. The same symptoms will appear as with soil plants but you can also check the roots. Healthy roots should be mostly white with maybe a slight yellowish tan tinge. If they are a brownish colour with dead tips or they easily pull away there is at least the beginnings of a serious problem. An organic dirtlike rotting smell means there is already a very good chance it is too late. As roots die and rot they eat Oxygen out of the water, as Oxygen levels are even further depleted more roots die, a viscius circle may be well under way. Reduced Oxygen levels and high temperatures both encourage anaerobic bacteria and fungi. The plants may still be saved but you will have to work fast.

3. How Hydrogen Peroxide prevents root rot/overwatering.
When plants are watered with H2O2 it will break down and release Oxygen into the area around the roots. This helps stop the Oxygen from being depleted in the water filled air spaces until air can get back into them. High Oxygen levels at the roots will encourage rapid healthy root growth. In a Hydroponic system H2O2 will disperse through out the system and raise Oxygen levels as it breaks down. Strong white healthy roots with lots of fuzzy new growth will be visible. This fuzzy growth has massive surface area allowing for rapid absorption of the huge amounts of water and nutrients needed for rapid top growth. A healthy plant starts with a healthy root system.

4. How to use it.
H2O2 comes in several different strengths 3%, 5%, 8% and 35%, also sold as food grade Hydrogen Peroxide. The most economical is 35% which we recommend be diluted to three percent before using, as at this high concentration it can cause damage to skin and clothing. When working with food grade H2O2 it is very important that you clean up any spills or splashes immediately, it will damage almost anything very quickly. This is extra important with skin and clothing. Skin will be temporarily bleached pure white if not washed cleaned. Gloves are strongly recommended when working with any strong chemical.

Food grade H2O2 can be diluted to three percent by mixing it one part to eleven parts water (preferably distilled). The storage container should be opaque to prevent light from getting in and it must be able to hold some pressure. If three-liter pop bottles are available in your area they are ideal for mixing and storing H2O2. There are twelve quarter liters (250ml) in three liters, if you put in one quarter liter H2O2 and eleven quarter liters (250ml) water in the bottle it will full of three percent H2O2 and the bottle can hold the pressure that the H2O2 will generate. Three percent Hydrogen Peroxide may be added at up to three ml’s per liter (2 12 tsp. Per gallon), but it is recommended that you start at a lower concentration and increase to full strength over a few weeks. Use every watering even on fresh cuttings. For hydroponics use every reservoir change and replace twenty-five percent (one quarter) every day. Example: In a 100L reservoir you would add three hundred ml’s (3%) H2O2 when changing the nutrient. You would then add seventy-five ml’s more every day.

5. Where to get it.
35% food grade: called food grade because it has no toxic impurities
Of course your local hydroponics retailer, whom you can locate over the web at www.hydromall.com. Direct order off the web (there may be shipping restrictions on high strength peroxides). H2O2 is used to bleach hair so the local hairdresser may have a source. The local feed supplier may have it in small towns. Prices range from fifteen dollars per quarter liter to eighty dollars a gallon. One gallon will treat up to fifty thousand liters of water.

3%5%, 8%
Can be found at most drugstores or pharmacies, prices start at a less than a dollar for a one hundred-ml bottle that will treat one hundred liters.

6. What to do if you already have root rot.

In Dirt:
Use peroxided water with anti-fungicide (benomyl) and a high Phosphate fertilizer (9-45-15, 10-52-10, 0-60-0) for root growth. Root booster (5-15-5) or any other product with rooting hormone dissolved in it is helpful in regrowing roots and is strongly recommended. If a plant is wilty adding Nutri-Boost may save it. Water heavily until liquid pours out the bottom of the pot. This sound like bad idea, but it flushes out stagnant dead water and replaces it with fresh highly oxygenated water. Don’t let plants sit in trays full of water, the soil will absorb this water and stay too wet. Don’t water again until the pot feels light and the top inch or two of the soil are dry.

In Hydro:
Change your nutrients. Add H2O2 to the system. This will add oxygen and chemically eat dead roots. If roots are badly rotted and can be pulled away by hand you should pull them off. They are already dead and will only rot, causing further problems. Add a fungicide to kill any fungus that is probably present in the rotted tissue to prevent it from spreading. Root booster will speed recovery. If plants are wilty Nutri-Boost may help save them. Increase aeration of the water, get an airpump and air stones, or more of them, for the reservoir. An air stone under every plant is usually very effective, but will require a larger air pump. Models that will do from forty to four hundred stones are available. Decrease the reservoir temperature, oxygen dissolves better in cold water and disease causing organisms reproduce slower as well. A good temperate range is 62F to 65F; anything above 70F will eventually cause a problem. It is also a good idea to remove any wilty plants from the system and put them on a separate reservoir so they don’t infect plants that are still healthy.

Summary
The key to big productive plants is a big healthy root system and Hydrogen Peroxide is a great way to keep your roots healthy. It is a must to ensure the biggest best crops possible and to increase the chances of your plants thriving to harvest. Peroxide users will rarely lose plants or crops to root disease and will harvest larger and more consistent crops.