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All Things Garden,  Beginner Basics,  Indoor Gardening

How to Prevent Green Algae or White Mold on Seedling Soil

Have you ever had a green substance grow on top of your seedling soil, and wondered “what’s up with that?” Well, you’re not alone! Our seed starting soil sometimes gets a little green tint too. Then folks always ask about it when they see our seedlings on Instagram, which is actually what inspired me to write this post. So, let’s do a quick Q&A about what that green stuff is, if it’s bad for your seedlings or not, and how to prevent or fix it! We’ll also talk about white mold on seedling soil.


What is the green stuff on top of my seedling soil?


It is mostly likely some sort of algae or moss growth, not mold. Algae appears as green residue or mossy-looking film. Mold will look more fuzzy, raised, lacy, and usually white, yellowish or gray in color. Algae is more closely related to plants, and requires sunlight or bright light to grow. On the other hand, mold is a fungi. It doesn’t need light to grow but does like moisture and organic matter. 


A tomato seedling in a 4 inch pot with the focus on the soil is shown. There is algae on the seedlings soil spread lightly across the top of the soil. In the background are a number of other tomato seedlings sitting under grow lights.
A little algae growth on one of our tomato seedlings.


What causes white mold or green algae on seedling soil?


Excess water, light exposure, poor air circulation, and/or humidity causes green algae on top of seedling soil.  I suspect that the presence of peat moss in most seed starting mediums has something to do with it as well. 

Algae growth occurs most often indoors or in greenhouse conditions. It’s especially common when the seedlings are very small, since the soil has more exposed surface area for light to reach. As your seedlings grow larger, shade out the soil, soak up water more quickly, and their roots begin to dominate the soil medium, the algae growth will usually fade away on its own. That’s what ours usually does!

Algae growth on seedling soil is a fairly common and natural occurrence, while mold may indicate your soil is contaminated or especially excessively wet. Using random soil to start seeds (e.g. soil from your yard, rather than a sterile bagged seed-starting mix) may lead to mold growth. 


Three small seedlings are shown sprouting out of a small block of soil. There is white mold all over the surface of the soil, not to be confused with algae on seedling soil which is much less of an issue.
White mold on seedling soil (source)


Is mold or algae bad for my seedlings?


Green algae or moss on the soil surface is generally not harmful to seedlings. Some sources say the presence of algae on the top of soil reduces important gas exchanges across the soil surface, and therefore may hinder the plant’s root growth. However, our seedling soil almost always gets a little algae – and our seedlings grow PLENTY big and strong! So as long as your seedlings look otherwise healthy and are growing well, I say don’t worry about it too much. 

In contrast, mold may be detrimental to seedlings. Mold on seedling soil indicates the presence of fungus. Not all fungus is bad, though some can lead to damping off: a condition where seedlings suddenly wilt and die (usually caused by fungal disease). It’s also bad to eat mold, and is especially concerning for seedlings you consume young and raw – such as microgreens.


8 Ways to Prevent Mold and Algae on Seedling Soil


Follow the tips below to prevent algae and mold growth in your seedling soil. Yet keep in mind that a little algae isn’t the end of the world! No matter our efforts to follow seed-starting best practices, we almost always end up with some. 


  1. Avoid overwatering. Seedlings like damp conditions, but not constantly soggy soil. Allow the soil to dry out slightly between watering. 

  2. Remove humidity domes right after seedlings sprout.

  3. Use a fresh, sterile, bagged seed-starting soil or medium to grow seedlings. This is especially important to prevent mold. 

  4. Water from below. Rather than spraying water from the top, pour water in a tray below your seedling containers. The soil will soak up as much as it needs through the drainage holes in the bottom of the containers. Only give them as much water as they can soak up within a few hours. Don’t let excess standing water sit. Start with just half an inch or two. (This also promotes deeper, stronger root growth. It’s the ONLY way we water seedlings after they sprout!) 

  5. Use an oscillating fan nearby to introduce good airflow and dry out the soil surface. The gentle wiggling of the plants also helps to strengthen their stems and is a great way to jump start the hardening off process. 

  6. Reduce heat. Seedling heat mats are a wonderful tool to use during seedling germination. They help expedite the sprouting process immensely! However, warm soil can also promote mold and algae growth. So, turn down or remove the heat mats after your seeds sprout.

  7. Boost seedling growth by feeding them with a dilute seaweed extract (once they’re at least several weeks old). In addition to helping them overcome any delays the algae or mold may cause, robust large seedlings also leave less room for the “bad guys” to thrive.

  8. Sanitize seed starting pots, trays and other supplies between uses or seasons – especially if mold has been an issue. Dilute bleach will kill fungi spores. Or, check out how we effectively sanitize our seedling supplies without bleach here.


As you can see, it’s a bit of a balancing act! For instance, reducing light is another “recommendation” I’ve seen to help reduce algae growth… but seedlings need light. Lots of light! In fact, seedlings thrive when provided at least 12 hours of very bright light (14 to 16 hours is even better). Too little light can easily lead to weak, leggy seedlings. So in that case, it’s clearly more important to provide ample light than to turn it down just to prevent algae.

 Learn more about using grow lights for seedlings in this post. 


A three tiered LED lighting plant rack with seedlings on each tier is shown inside a grow room. A standing fan is in the foreground offering some air circulation.
Good airflow and moderating water is key to preventing algae and mold. However, bright light can contribute to algae growth… but is essential for seedlings! It’s a worthy trade off. You can find our favorite LED grow light shelf here.


How to get rid of algae or mold on seedling soil


If you’ve already followed all the preventative tips above and are still seeing some mold or algae on your seedling soil, you can try to physically remove it if you wish. As we’ve established, you don’t necessarily need to worry about about algae – as long as your seedlings are healthy and growing! Yet if they seem to be struggling or the algae is especially thick and aggressive, go ahead and remove it.

Use an old butter knife, popsicle stick, or a similar firm, flat tool to gently scrape the algae off the soil surface. Don’t dig too deep and disrupt the roots! If needed, add a sprinkle of fresh seedling soil to replace the bit you removed from the top. Or, if the seedlings are about ready to be potted up, you can try to carefully remove the green algae during that process.

Mold is another story… The spores are likely spread throughout the soil, not just on top. You can still try to scrape it off, but advanced cases are more likely to come back. Like algae, a little bit may not be anything to stress over. Though if seedlings start dying (damping off) from mold, I recommend to start over with fresh seedling oil. Be sure to thoroughly sanitize your seedling containers between uses to kill any lingering fungal spores too!

One final option to get rid of mold on seedling soil is to utilize an organic fungicide spray.


A close up image of the tip of a butter knife scraping off the top portion of algae on seedlings soil.
Gently scraping and removing some algae from a pepper seedling (which honestly I would have otherwise left, but did as a demo for this post). The soil is clearly very wet too. We just under-watered that morning, but will let it dry out quite a bit before watering again.


I hope that answers all your questions!


In summary, mold and algae are fairly common on seedling soil, but mold is the more risky of the two. Both can usually be controlled with good airflow, reducing water, using fresh seedling soil, and other easy measures. If you’re experiencing algae on your seedlings right now, I hope it makes you feel a little better that us experienced gardeners get it too! Please let us know if you have any additional questions or tips in the comments below. Also, please consider pinning or sharing this article if you found it useful. Thanks for stopping by!


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5 Comments

  • Virtso

    I actually had some algae growth that has gone away with time and was wondering about that. It didn’t impact the various seedlings, and they are growing fine. I also got a bit of white “fuzz” like lace over the corn when it started to sprout, but this went away in a few days. I’m not sure if some spiders got into the greenhouse or if it was something due to the humidity, but it has not come back. The article was very helpful!

  • Heather

    I have actually gotten lichen growing on top of mine before! I scraped it off. It’s good to know that algae is harmless, thank you.

  • Rocio Velis

    The article was very timely, I’m seeing a small film of white over my peppers soil and was unsure of what to do. I really hope I don’t have to start over.
    Do you think re potting could help?

    • Aaron (Mr. DeannaCat)

      Hello Rocio, I would try and somewhat scrape off the white film and use some of the tips in the article to see if you can eliminate the problem before having to repot. If the film comes back I would then repot them into another container if their root ball is close to maxing out their current containers. Hope that helps and good luck!

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