Seed Starting Tips: How to Prevent and Manage Algae Growth

Its that time of year again where we have purchased our seeds and now we are planning our seed starting schedule. We have already started several trays of lisianthus seeds. I just went out to check on them this morning and I found Algae in the trays. So today we will be talking all things ALGAE!

Starting seeds indoors is an exciting part of the growing season, but it comes with its own set of challenges—one of the most common being algae growth. If you’ve ever noticed a green, slimy film forming on the surface of your seed-starting mix, you’re not alone! While algae won’t necessarily kill your seedlings, it can create problems by competing for nutrients, reducing airflow, and increasing moisture-related issues like damping off.

In this post, we’ll cover why algae forms, how to prevent it, and what to do if it appears—so you can keep your seedlings healthy and thriving!

Why Does Algae Grow in Seed Trays?

Algae are simple, plant-like organisms that thrive in moist, nutrient-rich environments with plenty of light. Unfortunately, seed-starting trays provide the perfect conditions for algae growth, especially when:

• There is too much moisture in the soil.

• The trays are exposed to high humidity and poor airflow.

• There is an excess of nutrients, especially from fertilizers.

• Seed trays are placed under constant light with no dark periods.

While algae itself doesn’t harm seedlings directly, it can block oxygen from reaching roots, encourage fungal diseases, and create a crusty surface that makes it harder for seeds to germinate.

How to Prevent Algae Growth in Seed Trays

The best way to deal with algae is to prevent it from forming in the first place. Here are my top tips to keep your seed trays clean and algae-free:

1. Avoid Overwatering

• Algae thrives in excess moisture, so aim to keep soil damp but not soggy.

• Water from the bottom whenever possible to keep the soil surface drier.

• Allow the top layer of soil to dry slightly between waterings.

2. Improve Airflow

• Use a small fan near your seedlings to increase air circulation and reduce excess moisture.

• Keep seedlings in a well-ventilated space to prevent stagnant air.

3. Use a Sterile, Well-Draining Seed-Starting Mix

• Avoid using soil that retains too much moisture or contains organic matter that feeds algae.

• Consider mixing in perlite or vermiculite to improve drainage.

4. Reduce Excess Light Exposure

• While seedlings need 12-16 hours of light per day, 24-hour light exposure can encourage algae growth.

• Use a timer to ensure a natural light cycle with dark periods.

5. Be Cautious with Fertilizer

• Algae feeds on nutrients, so avoid fertilizing too soon—wait until seedlings develop their first true leaves.

• If fertilizing early, use a diluted, low-strength liquid fertilizer to prevent excess nutrients from accumulating.

6. Sanitize Your Seed Trays

• Always start with clean trays and tools to prevent introducing algae spores.

• Wash seed trays between uses with a diluted hydrogen peroxide or bleach solution (1 part bleach to 9 parts water).

What to Do If You Already Have Algae in Your Seed Trays

If you notice algae forming, don’t panic! Here’s how to remove it and prevent it from coming back:

1. Gently Scrape Off the Algae

• Use a small fork, toothpick, or even your fingers to lightly loosen and remove the algae without disturbing the seedlings.

• If the algae layer is thick, you may need to gently scrape off the top layer of soil and replace it with fresh, sterile seed-starting mix.

2. Improve Drying Conditions

• Reduce overwatering and allow the top of the soil to dry slightly between waterings.

• If possible, remove the humidity dome for a few hours each day to let excess moisture escape.

3. Increase Air Circulation

• Place a small fan near your seedlings to help dry the surface and reduce humidity.

• Adjust your seed trays to ensure they are not too crowded, which can trap moisture.

4. Apply a Natural Algae Treatment

If algae continues to be a problem, try one of these gentle treatments:

• Cinnamon: A light dusting of cinnamon on the soil surface can help prevent algae and fungal growth.

• Diluted Hydrogen Peroxide (H2O2): Mix 1 part hydrogen peroxide (3%) with 4 parts water and spray lightly on the soil surface. This helps kill algae without harming seedlings.

• Chamomile Tea Spray: Brew a weak chamomile tea and mist it over the affected area—it has natural antifungal and antibacterial properties.

5. Repot If Necessary

• If algae is persistent and affecting seedling growth, consider transplanting seedlings into fresh, sterile soil to give them a clean start.

WE HAVE ALGAE IN OUR TRAYS RIGHT NOW, AND OUR SEEDS AREN'T READY TO BE REPOTTED. THE SEEDLINGS ONLY HAVE ONE SET OF LEAVES AND I DON'T WANT TO DAMAGE THEM, SO WE ARE GOING ADD A LAYER OF VERMICULITE TO THE TOP OF THE SOIL WHERE WE HAVE SEEDLINGS.

I have noticed that I get the most algae in my Lisianthus Seedlings, and Eucalyptus Seedlings.

Why Is Lisianthus Especially Susceptible to Algae?

Lisianthus is a notoriously slow-growing flower, and its specific germination and growth requirements create the perfect conditions for algae to thrive.

1. Long Germination Time & High Humidity

Lisianthus seeds take up to two weeks (or longer!) to germinate, and during this time, growers often keep them covered with a humidity dome to maintain the moisture and warmth needed for successful sprouting. However, this extended period of high humidity and stagnant air creates an ideal environment for algae to form. Unlike faster-germinating seeds, which quickly sprout and reduce excess moisture through their own water uptake, Lisianthus sits in a damp, warm environment for a prolonged time—allowing algae to establish itself.

2. Slow Growth & Lack of Canopy

Even after germination, Lisianthus seedlings remain extremely slow-growing. They take weeks to develop their first set of true leaves, and even longer before they put on substantial growth. Since they remain small for so long, they don’t create a leafy canopy to shade the soil. This means the surface of the seed-starting mix is continually exposed to bright grow lights, which further encourages algae growth. In contrast, faster-growing seedlings will quickly develop leaves that cover the soil, helping block light and suppress algae.

3. Consistently Moist Soil

Since Lisianthus has delicate, shallow roots early on, growers tend to keep the soil consistently moist but not soggy to support even growth. This careful watering is necessary but also means the soil surface rarely dries out completely, which is another factor that allows algae to thrive.

How to Prevent Algae in Lisianthus Trays

Because Lisianthus seedlings take so long to develop, it’s important to take extra steps to prevent algae from forming in their trays. Here are a few targeted strategies:

• Ventilation Is Key – If using a humidity dome, remove it for a short period each day to allow excess moisture to escape.

• Increase Air Circulation – A small fan placed near your trays can help keep moisture from becoming stagnant.

• Use a Light Dusting of Vermiculite – Sprinkling a fine layer of vermiculite on the soil surface can help absorb excess moisture and reduce light exposure to the soil.

• Bottom Water Instead of Overhead Watering – This keeps the soil surface drier while still hydrating the roots.

• Use Natural Algae Prevention Methods – A light dusting of cinnamon or an occasional misting with diluted hydrogen peroxide can help prevent algae without harming delicate Lisianthus seedlings.

This section adds depth to your blog post by addressing why Lisianthus is particularly prone to algae and how growers can take extra precautions. Would you like me to expand on anything else?

Algae growth in seed trays is a common issue, but with the right watering techniques, airflow, and sanitation practices, it can be easily prevented and managed. By keeping your seed-starting environment balanced, you’ll give your seedlings the best chance to grow strong and healthy—without the competition from unwanted green slime!

Have you ever battled algae in your seed trays? Let me know your best tips in the comments!