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Home  / Know Your Roots: Pinetree Garden Blog
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What’s Wrong with My Seedlings?

4 min read 22 Comments

What’s Wrong with My Seedlings?

When gardening, it’s an unavoidable fact that you will have successes as well as failures. Failures can be caused by an outside force you have no control over (cat digging up your seedlings, a tray of tiny green shoots getting knocked off the table by accident, etc.), but it can also be caused by things you do have control over. Overwatering, under watering, not enough light, and more. These mistakes are very common, and not something to feel bad about!

1. Seeds fail to germinate?

What’s Wrong with My Seedlings?

Possible Causes

  • Temperature of the soil is too hot or too cold. Most seeds like a soil temperature of around 65°-75°F. In general, 

  • the warmer the temperature, the faster the seed will germinate. Please note that even if the air feels warm, the soil may still be chilly. We often recommend a bottom heat source. 
  • Seeds rotting in the soil means it was too wet. Your soil should be moist, but not soaked.
  • Planting depth of the seeds – plant too deeply, and germinating seeds have a hard time reaching the surface or light is unable to reach the seed. Plant too shallow, and too much light can damage the seed. Most seed packets will instruct you on how deep to plant your seed!
  • Growing medium was allowed to dry out. Your soil should remain moistened but not drenched, and not bone dry.
  • ‘Damping off’ disease, which can affect the seeds before they germinate. Damping off occurs when a pathogen that thrives on too-wet conditions is able to grow and kill the seeds before they can emerge.
  • Remember - Pinetree stands behind its products! We will always work with you if you have concerns about germination of seeds you have purchased from us. 

    2. Seedlings fall over or start to decay at soil level

    What’s Wrong with My Seedlings?

     

     

    This is a sign of damping-off disease (fungus organisms that attack seeds and young seedlings, ultimately killing them). Some causes of damping-off are:

    • Cold, wet soil
    • Poor soil drainage
    • Poor air circulation
    • Unsterilized soil mix, or reusing soil from previous seed starting
    • Dirty growing containers
    • Stress from low light

     

     

     

     

    3. Leaves start to curl under, growth appears stunted or dwarfed

    What’s Wrong with My Seedlings?

    Possible Causes

    • Too much light. Seedlings need a ‘rest’ period, which is why it is suggested to only provide 14-16 hours of light.
    • Over or under fertilization. Too little nutrients can stunt growth, too much nutrition can damage the roots and prevent the seedling from taking in water.
    • Low temperatures. Most seeds like a soil temperature of around 65°-75°.
    • Excessive moisture and overwatering. If the soil remains consistently wet, it can rot the roots and prevent the seed from taking in water. It may look like your seed needs water, but in actuality, it needs anything but! Make sure to test the moisture of your soil by feeling with your fingers. Soil should be moist but not soaked.

     

     

     

     

    4. Seedlings have pale, discolored leaves; or leggy, spindly growth

    Possible Causes

    What’s Wrong with My Seedlings?
    • Insufficient lighting, or light source too far from your seedlings
    • Fertilizer burn from adding too much fertilizer, which can damage the plant's root system
    • Excessive watering
    • Nutrient deficiency – check the growing medium you are using to find out if nutrients are supplied in the mix. Some have tiny amounts to just get seedlings going, which means you then have to supply the rest until planted out in the garden.
    • Overcrowding of seedlings. Be sure to thin your seedlings to prevent this.
    • Temperatures too high. Most seeds like a soil temperature of around 65°-75°.

     

     

     

    5. When transplanting, you see poorly developed root systems

    Possible Causes

    What’s Wrong with My Seedlings?
    • Poor drainage
    • Low soil fertility
    • Damage from fertilizer salts, a.k.a. ‘fertilizer burn’, by adding too much fertilizer
    • Low soil temperatures. Most seeds like a soil temperature of around 65°-75°.
    • Compacted soil (lack of air space in growing medium), which can arise from overwatering and poor drainage.

     

     

     

     

     

     

    6. Moss or mold is growing on your medium

    What’s Wrong with My Seedlings?

    Possible Causes

    • Lack of air circulation. Set a fan up to move air around your plants
    • Excessive moisture. If the soil remains consistently wet, it can rot the roots and prevent the seed from taking in water. It may look like your seed needs water, but in actuality, it needs anything but! Make sure to test the moisture of your soil by feeling with your fingers. Soil should be moist but not soaked.

     

     

     

     

     

     

     

    7. Try playing some tunes for your seedlings!

    We know that there is no proof to back this up, but have you thought about playing some of Pinetree's certified Spotify playlists to help the seedlings grow? 

     

     

     

     

    Here’s a short message of encouragement from our master gardener, Jaci:

    “As a gardener, I know how discouraging it can be when some seedlings fail or don’t look perfect. Try not to dwell on it too long; just take the opportunity to gain some knowledge on the possible underlying causes so you can be successful in the seasons ahead. I have been gardening for nearly 20 years, and each year still brings new learning experiences for me.”

     

    Some quick tips for making sure your seedlings flourish!

    • Once your seedlings have 2-3 sets of leaves, the most important thing to do at this point is to supplement them with nutrients! Most seed starting mixes have very little nutrition if any at all. We suggest using ¼ to ½ strength liquid fish/seaweed fertilizer every other watering for your seedlings to be at their happiest!
    • Using a soilless seed starting mix to start seeds is very important. Soilless seed starting mix is light, fluffy, and perfect for your seedlings to grow strong, sturdy roots! Garden soil or potting soil is often far too heavy and lacking in drainage, making it hard on the delicate root systems of the young seedlings.

    What are your favorite tips and tricks for seed starting?


    22 Responses

    Donna Dawson
    Donna Dawson

    April 28, 2022

    i see why mine are not thriving …. i have the grow light on 24/7…….can they recover now that i know to turn it off? UGH

    Prithvi Hanspal
    Prithvi Hanspal

    April 05, 2022

    Very helpful instructions and information I will use them in my experience Thank you

    Meagan Summers
    Meagan Summers

    January 25, 2022

    Oh no! I just watered all my germinated seeds again because the soil looked dry. I turned on the fan but I watered them really well and I’ve been watering them every 2-3 days which I’m guessing is too much. Man!

    Grow Guru
    Grow Guru

    January 25, 2022

    It was interesting to learn all causes of seedling fail that you have explained. I like how you explain every cause with reason. Grow Guru provides you the best quality and variety of Hydroponic Systems like seeds, nutrients that extends the life of your garden. Visit our website for more info! https://growguru.co.za/

    Jayde Vaux
    Jayde Vaux

    January 25, 2022

    Thank you to all the comments you’ve helped massively I started gardening last year and I’m struggling with my seedlings they have got 2 leaves on all seedlings but they’re not happy I’ve checked all the list above and I’m thinking it’s the light issue unfortunately it’s to cold here to put them outside I’ve got a lighting system and I’ve also got heat pad
    Maybe it’s the watering
    My begonia isn’t doing anything my strawberries have decided to rot but I’m guessing that maybe it was the crown under soil I wish I had someone here that could help me but covid has stopped that. Unfortunately so I only have these great sites

    Jewel
    Jewel

    July 17, 2020

    I had those little gnats this year. It’s bad news if you have them! They lay eggs and the larva are in the soil and eat the roots. I had 6 inch plants that should have had a large root system hardly had anything. I tried treating the soil and plants (above the soil) with non toxic dish soap suds, and even watering the plants with the soapy water, then flushing out the soap after 15 minutes or so. It seemed to really take care of the problem.

    Chris Hunt-Lex.,NC
    Chris Hunt-Lex.,NC

    July 17, 2020

    My seeds did great and are already producing, won’t be long before we have to freeze and can, thanks for the article….

    Vanessa
    Vanessa

    February 10, 2020

    This was helpful in that I believe I need to fertilize, going by the suggestions. I see the person writing this has been gardening for 20 years. That’s commendable! I have been gardening for 45 years—-still learning! I used to be able to start my seeds in my growing medium and not worry, not any more. The new mediums out there just don’t have the nutrients my old one did. At least that’s how it seems to me. Thanks for the article. It was helpful.

    Sara Clay
    Sara Clay

    February 10, 2020

    At first sign of damping off, water from top with chamomile even if they don’t need water, drain well and do not rewater til soil is on the dry side. Has worked for me to save most of the damping off seedlings!

    I start all my seeds in pure compost from my piles, screened through 1/4” hardware cloth, with a sprinkle of bone meal mixed in. If snow melt here in Vermont is late and even raised beds are too wet to work, they get weekly fish emulsion to keep them vigorously growing, or even potting up for those that like warm soil. So I take care not to start seed too early since younger vigorous transplants do better than older root-bound ones.

    No need to buy that expensive sterile nutrient-less starting mix that dries out so fast if you have compost that stays so nicely moist and is forgiving if neglected for a day or three. I bring in several 5 gallon buckets full each fall and store in cool cellar with an old dinner plate on top so it has a bit of air around the edges and stays damp but not moldy. The worms (and no doubt the beneficial bacteria and fungi) are still living when I start my seeds in spring. I put the worms in kitchen compost and dump them into the outdoor pile.

    Only had damping off 2 years out of almost 30 here, and the chamomile tea did the trick for most of the seedlings.

    Linda Paulson
    Linda Paulson

    February 10, 2020

    Potting soil also causes little flying bugs similar to fruit flys

    Wilma Crumling
    Wilma Crumling

    February 10, 2020

    Excited about gardening this year!

    Frank Heiberger
    Frank Heiberger

    February 10, 2020

    The only time you water from the top is when you water the seeds in initially. From then on, whether seeds have sprouted or not, water from the bottom to draw the roots down and create strong root systems It’s time to water when you lift a pot or six-pack and the tray beneath it is no longer damp. Add only enough water to fill the tray about 1/4 inch.

    Susan Hatfield
    Susan Hatfield

    February 10, 2020

    Thanks, great information. Love the music!

    Amy
    Amy

    February 10, 2020

    Thanks for the info. Just in time. Also love you choice of music! But really thank you for the information.

    Katie Pence
    Katie Pence

    February 10, 2020

    To deter mice and birds I sprinkle chili powder or cayenne pepper on the flats. Doesn’t seem to affect the plants. But does help if your seedlings are getting g eaten.

    Kath Anderson
    Kath Anderson

    February 10, 2020

    What a great article to read on this February morning in Minnesota! Will be starting seeds when we get back from a week in Florida. No new information for me but lots of good reminders. I LOVED the Spotify playlist, you guys rock!

    Ruth Flescher
    Ruth Flescher

    February 10, 2020

    My favorite watering tool for starting seeds is a kitchen baster. It lets you put the water exactly where you want it (on the soil, not the seedlings) and you can control the pressure to apply the water very gently so seedlings aren’t knocked over and soil and seeds aren’t washed out of place.

    Julie Wolf
    Julie Wolf

    February 10, 2020

    I start tomato seedlings by planting the seeds in small pots,moistening the soil well,covering with plastic wrap, and putting on top of the refrigerator. The heat from the refrigerator makes the seeds germinate quickly, and I then move them to a sunny window.

    Jana
    Jana

    February 10, 2020

    Very helpful tips! Thanks for this article.

    Thomas F Witwicki
    Thomas F Witwicki

    February 10, 2020

    This is an excellent article. In my 40 plus years of gardening, I have experienced just about every problem you mention. I have found that the use of heat mats is critical for the proper germination of some heat loving plants. Always consult the optimal germination temperature range for the vegetable or flower to be germinated. Using a 20 row seeder with a humidity dome as you have pictured can optimize the space on a heat mat, but be careful that you don’t mix seeds that require different germination temperatures or germination times, because the humidity dome needs to come off once you see the seeds start to germinate.

    Bob
    Bob

    February 10, 2020

    Cinnamon sprinkled on the soil around seedlings can prevent damping off (plant rotting at soil level).

    Richard Mammel
    Richard Mammel

    February 10, 2020

    As always, you wonderful folks hatch such good stuff. This straightforward list, the hints, and very helpful pics in all compress a lot of instruction into a nearly Spartan space. This is a good presentation for even veteran gardeners, well beyond novices, being at the least alerts as to how problems may occur and how to remedy those that may present themselves. Thanks as always to you!

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