How to Prevent Mold & Algae on Seedlings

Starting your plants from seeds is a great way to get a jump start on the growing season. 

The little sprouts that you are growing are very sensitive to changes in conditions like humidity and moisture.  This can lead to the mold and algae you might see on seedlings but there are ways to prevent it or get rid of.

Mold and Algae on Seedlings

You have two weeks before you can transplant your seedlings outside and one day you notice that the top of the plugs is covered in mold and algae.  This means they have fruiting bodies or a green film.  What should you do?  Should you treat this?  Should you throw away the seedlings away and start over?  Should you try to transplant them in new soil and let them continue to mature?

If your seedlings have mold or algae, it can become an issue that can be bad enough to keep the crown of the seedling moist, encouraging plant disease or smother the seedling.  The crown is where the stem meets the media.

Identifying Mold and Algae

  • Mold:  This will be evident from the fruiting bodies.  They usually form a fuzzy-looking mass on top of the plugs or crowns
  • Algae:  This is usually a green slim on the top of the seedlings.  It may also be a bloom of green, brownish, or pink sticky material that sprawls across the soil surface.

Algae: What to Do

No matter if it is a small or large hydroponic system, algae can be a problem.  It can be easily controlled if you limit the light that shines on the growing substrate.  The bad thing is that for seedling growth light is necessary.  When adjusting the light, you want to keep the light levels high enough to keep the seedlings growing but then you want to decrease it to prevent algae from growing.  To accomplish this, use the seedlings to shade out the algae.

When you have the right growing conditions, they will grow tall enough to shade out the top of the crowns so the algae will not be able to grow there.  Algae should not be a problem if you give the seedlings enough air movement, nutrients, and adequate light.  

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Algae can also be caused by high moisture, which occurs from over-watering.  To make sure that your seedlings are not too wet you need to reduce watering.  This means to increase the time between watering.  Make sure that the media you use drains easily.  Some use a humidity done to help prevent the soil from drying out so you do not need to water them too much.

  • Use a good quality seed starting soil but not garden soil.  This is because disease and spores could be found in the garden soil.
  • You should only water when the soil surface is almost dry.  Do not let them set in a pool of water

When you notice algae on the soil, you can scrape off the soil that is affected.  If the seedlings are large enough, you could completely repot the seedlings but there is a chance you could damage the new roots so be careful if you transplant them.  You can also rough up the soil to prevent it from staying too wet.  A home remedy that you can use is to sprinkle a little cinnamon on the soil surface to get rid of algae.


Mold:  What to Do

When you have mold on seedlings, it happened because the media you used is contaminated.  The first thing to do is to use high-quality media, which means using a brand-name media.  The media you use should be sterilized.  To sterilize, mix one cup of bleach to nine cups of water and soak the seedling flats for 30 minutes, rinse in clean water, and let them air dry before you add the soil.

Although the mold will not harm the seedlings, this is a sign that the growing conditions are not right.  If you see a brownish or white mold, it means that there is a saprophytic fungus.  They do not attack the living tissue of the seedlings but it can make it hard for them to germinate.  Sometimes you can remove this mold by agitating the surface of the soil.

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When you have mold in the soil, it means it is too wet.  Although they appear to be growing and looking healthy, they are at a risk to develop damping-off.  It will cause the stems to collapse and the seedlings will die.  Mold can also develop because of being in an excessive warm spot.  There will be a crust on the soil so the water will not penetrate, which blocks germinating seeds.

If you remove the mold from the soil you risk harming the seedlings.  To keep it from increasing, let the soil dry before you water it.  You should also reduce the amount of water you give them so the soil is not soggy but just damp.

 Mold or Algae:  What to Do

For algae, mold, other pest problems, and diseases, the biggest problem is excess moisture.  The top of the plugs of seedlings should be allowed to dry between watering.  Never allow the plugs to always be wet.  Another good practice is to push seedling growth as much as you can.  When you have mature seedlings, they not only shade out the algae but they also reduce the seedling’s susceptibility to mold and algae.  


If you can transplant your seedlings a week or two early, there is less chance for them to be infected by algae and mold.  Make sure that you are not over-watering your seedlings and that they are not getting too much heat.  All of these things can promote mold and algae.  If you can prevent it from happening, it will be easier than trying to get rid of either of them.  Preventing mold and algae will make your seedlings stronger and healthier so they will survive once you transplant them outside.