Garden Planning?

What’s Wrong with my Seedling? Fix Seed Starting Problems

Wouldn’t it be nice if you could just throw seeds in the dirt and they’d happily grow?

Unfortunately it’s not that easy and seed starting problems are common. From seeds not germinating, plants disappearing, mold on the soil or seedlings collapsing, there are many things gardeners have to deal with once you start sowing seeds.

I’d like to help you troubleshoot those seed starting problems

Common seedling problems discussed today:

  • Why did my seeds not sprout?
  • Why are my seedlings leggy?
  • How come my seeds rotting?
  • Why did my seedling collapse?
  • Where did my seedlings go?
  • What ate my seedlings?
  • Why is there mold on the soil?
  • How do I stop damping off?
  • Why do my seedlings fall over and die?

Find out what is wrong with your seedlings: from damping off, gnats, over watering and no germination

Why did my seeds not sprout?

There are a few reasons that your seeds didn’t sprout. The most common reasons:

  • The seeds were too old. You can germinate old seeds, but often they have less plant vigor. Just because they are old, doesn’t mean they won’t sprout, however in general older seeds have lower germination rates over time, which means if you sowed 30 seeds, maybe only 10 germinated if they are older than a few years. This depends on how they were stored and the type of plant. I’ve written about using old seeds in this  ‘should you use old seeds?’.
  • The seeds were sown too deeply into the soil. This is a very common mistake, people sow seeds too deeply. Be sure to carefully read the seed packets and make sure you’re sowing at the right depth. Tiny seeds like carrots or lettuce only barely need to be covered with dirt.
  • Someone stole the seeds. If you sowed your seeds outside, it’s possible that a critter stole the seeds. Seeds like sprouted peas or corn are often taken by birds or squirrels.
  • Washed away. Seeds sown outside right before heavy rains might have been washed away. If the soil in your garden beds looks disturbed after heavy rainfalls that might be cause of seeds not germinating.

Over watering can cause many seed starting problems

Why are my seeds rotting?

The most common reason why seeds rot is overwatering. This is a problem both inside and outside.

Over watering is the most common seedling mistake which then creates other problems, from root rot, mold to gnats and damping off.

Your seedlings need water, but let the soil dry out in between watering and make sure you have a fan going for air circulation. There are also some neat seed starting trays where you water from the bottom instead of the top. Some people just use a spray bottle and mist the plants, but that’s a lot of work.

Because so many seedling problems are related water saturated soil, it can really help to water from the bottom

A bottom watering tray can help to reduce many seedling over watering problems

Burpee Bottom watering tray

The Growease Seed Starting Tray

Tips for preventing leggy seedlings

Why are my seedlings leggy?

Leggy seedlings are when the plant is long and thin and not growing straight up. This is really easy to happen for the following reasons:

  • The light source is too far away and the plant is reaching for light. If you have grow lights it’s better to have them a few inches above the plants and raise them as the plant grows.
  • The plants are overcrowded. Although growing densely is great for indoor microgreens, the plants become stressed and compete for light and resources creating leggy plants. Be sure to thin out your seedlings.
  • They need wind for strength. Plants grown outside are faced with windy days which in turn create a stronger thicker stem. When you grow inside you need to ‘create wind’ by adding a fan. A fan is not only great for air circulation, it also helps with preventing leggy seedlings. Some people also swear by ‘brushing’ the seedlings to simulate wind too. Below you can see tomatoes that weren’t grown with  fan and are reaching too high for the light source growing thin instead of having a thick stem.

Leggy tomatoes

If you have leggy seedlings you CAN save them!

The trick is to re-pot your seedlings so that most of the thin leggy part is in the soil. Here are my tips for re-potting seedlings.

How to repot leggy seedlings to save them!

Why did my seedling collapse?

damping off & gnats

Gnats are similar to fruit flies and love to lay eggs in your soggy wet soil. These fungus gnats will feed on your seedling and cause it to collapse, creating ‘damping off’ which is where you’ll see your seedling bent in the middle. Damping off will kill your seedlings and can spread to your other plants within a day or two destroying your precious seedlings.

Here are few ways to prevent fungus gnats:

  • Don’t over water! They love wet soil so over watering is a major preventative step.
  • Sprinkle cinnamon. I learned this trick years ago from the Small Foot Print Family who has an in-depth post on fungus gnats.
  • Disinfect Seeding Trays. Learn how to here.To prevent fungus and soil problems make sure you clean and disinfect old seeding trays.
  • Air Flow. Just as a fan is important to prevent leggy seedlings, having good air flow is important for preventing fungal problems.

How to stop and prevent damping off and gnats naturally

Other seed starting problems

Mold on the soil is caused from over watering, not having air flow and not disinfecting your pots. If your seeds or roots are rotting that’s also caused from over watering and not enough drainage. Be sure to use seed starter soil because it’s nice and loose and allows for root expansion.

Learn more seed starting tips in my free seed starting 101 guide for beginners.

How to prevent and fix leggy seedlings


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  1. Thank you for this article. I’m growing all my vegetables from seed this year and boy are they leggy. I adjusted my grow lights and provided circulation. Thanks for the tips. I also try the cinnamon if needed.

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