Help with seedlings, and how to fix common seed starting problems

Help with seedlings, and how to fix common seed starting problems

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Help! What is wrong with my seedlings? This is one of the most common question I get from gardeners when they’re starting seeds indoors. If this sounds familiar, and you need help with seedlings, then you’ve come to the right place. This troubleshooting guide will help you figure out why your seedlings are struggling (or worse, falling over and dying), and give you tons of tips for how you can fix common seed starting problems.

Healthy seedlings growing indoors

Healthy seedlings growing indoors

If you’re struggling with growing seeds indoors, you’re not alone. We have all been there, and everyone who has ever started seeds indoors has had seedling problems at some point (even the seasoned experts!). The good news is that many of the issues are easily fixable with a few minor adjustments. First, let’s talk about the top most common problems that gardeners have when starting seeds indoors, then we’ll get into troubleshooting and help with seedlings.

5 Most common seed starting problems

  • Seedling damping off – Probably the biggest frustration for gardeners is when their seedlings tip over at the base and die without warning. This is called damping off, and is caused by seedling blight. Damping off is the most common cause of seedling death.
  • Discolored or faded leaves – When seedlings leaves turn brown, yellow, white, or look dull and faded, that’s a sure sign that something is wrong. Most of the time, you can save your seedlings but you have to act fast.
  • Weak, leggy seedlings – If seedlings don’t get enough light, they will reach and stretch for the brightest light source that’s nearby (usually a window). Easily fixable, but if nothing changes, it won’t take long before seedlings grow tall, leggy, and too weak to recover.
Severely leggy seedlings won't recover

Severely leggy seedlings won’t recover

  • Mold growth in seed trays – Mold usually grows on top of the soil in seed trays, but it could grow on seedlings too. The mold isn’t directly what causes seedlings to die, it’s a symptom of other problems. And if those issues aren’t fixed, your seedlings could eventually die.
  • Tiny bugs flying around – Soil gnats (aka fungus gnats) are tiny bugs that lay their eggs in soil, and they are a common pest indoors. You’ll see soil gnats (often mistaken for fruit flies) flying around the seed trays, or crawling in the soil. They’re normally just a nuisance, and won’t damage the seedlings if kept under control, but they are a sign of a bigger problem.

Help with seedlings, and how to fix problems

The good news is that most of these common seedling problems are easily fixable, but you will need to take action pretty quickly to save your seedlings. So now let’s dig into the help with seedlings part. Below I will walk you through each of the common problems, identifying the main causes, and their solutions.

Seedling damping off

Unfortunately, damping off happens so fast that there’s really no way to save the seedlings once they flop over. The best way to stop damping off is to prevent it from happening in the first place. Here are the common causes of damping off, and their solutions.

  • Using the wrong type of soil – Solution: Always use a quality seed starting medium or pellets for growing seeds. Don’t use regular potting soil, and never reuse any of your soil or pellets.
  • Seed starting equipment wasn’t sterile – Solution: Disinfect all dirty seed trays, plastic cells, lids, and plastic seedling pots before using them to grow seeds. Soak your equipment in a solution of one part bleach to nine parts water to disinfect them.
Disinfect seed starting trays to prevent damping off

Disinfect seed starting trays to prevent damping off

  • Not enough ventilation – Solution: Remove the seed tray lids once the seeds have germinated. Keep an oscillating fan blowing over the seedlings to ensure proper ventilation.
  • Soil kept too wet – Solution: Don’t water your seedlings if the soil is already wet or soggy. Don’t allow the containers to sit in water for extended periods of time.
  • Watering from the top – Solution: It’s best to water your seedlings from the bottom by pouring water into the seedling tray, and allowing the soil to absorb the water from the bottom. Empty any water that hasn’t been soaked up after 30 minutes.

Discolored or faded leaves

Once you notice that seedling leaves have started to fade or change color, it’s important to figure out what’s wrong and fix it quickly. Many times you can save your seedlings, but if the damage is severe, some seedlings may not recover. These are the most common causes of discolored or faded leaves, and the solutions for how to save your seedlings…

  • Overwatering – Solution: Make sure the soil is never saturated or soggy, and drain excess water from the seed trays.
  • Fertilizer burn – Solution: Chemical fertilizers are notorious for burning tender seedlings. Switch to natural, organic fertilizers rather than using chemical fertilizers. Always follow instructions on the fertilizer package.
  • Sunburn – Solution: Move your seedlings out of the sun immediately (severe sunburn is usually fatal to seedlings). Always be sure to harden off your seedling properly before moving them outdoors or into direct sunlight.
Always use quality seedling soil mix

Always use quality seedling soil mix

Weak, leggy seedlings

This is definitely one of the biggest problems with seedlings growing indoors, and also one of the easiest ones to fix. However, if you don’t fix the issue that’s causing seedlings to grow tall and leggy, they will eventually grow too weak to survive. If your seedlings have grown so tall that they are falling over… then it’s probably too late to save them. Here are the main causes of weak, leggy seedlings, and how to fix them…

  • Seedlings aren’t getting enough light – Solution: Add a grow light and position it so it sits 2-4 inches above the seedlings at all times, and keep it on for 14-16 hours per day. You can buy a grow light system to make this super easy, or make your own grow lights for seedlings using a fluorescent light fixture and plant grow light bulbs. It’s also helpful to use an inexpensive outlet timer so you can set it and forget it. Learn more about grow lights for seedlings.
  • Seedlings are overcrowded and competing for light – Solution: Thin your seedlings by cutting out the weakest ones at the soil level so there’s only one growing per cell or pellet (never pull them out of the soil). If your seedlings have outgrown the seed trays, then it’s time to transplant them up into seedling pots.
Starting seeds under lights prevents leggy seedlings

Starting seeds under lights prevents leggy seedlings

Mold growth in seed trays

As I mentioned above, it’s not the mold growing in your seed trays that will kill your seedlings… it’s the problem(s) that is causing the mold that you have to be worried about. Once you fix the problem(s), the mold will die. You can carefully scrape the mold off the soil to help get rid of it. Below are the causes of mold growth in seed trays, and how to fix them…

  • Overwatering – Solution: Make sure the soil is never soggy or kept constantly wet, and try to allow the very top layer of the soil to dry out a bit between waterings. Water seed starting trays from the bottom rather than the top.
  • Seedlings are overcrowded – Solution: Thin out your seedlings so there’s only one growing per cell or pellet. Otherwise, pot up your seedlings if they have outgrown their seed tray.
  • Not enough air circulation – Solution: Add an oscillating fan and position it to blow over your seedlings to give them plenty of airflow, and help to dry out soggy soil.
Use a fan to help with seedlings health

Use a fan to help with seedlings health

Tiny bugs flying around (soil gnats)

The presence of soil gnats is another symptom that something more serious is wrong with your seedlings. Soil gnats feed on rotting organic material, including unhealthy seedling roots. They are usually just a nuisance, and rarely cause fatal damage to a plant. But if the infestation is severe, then you need to take quick action. There is one main problem that causes soil gnats to infest your seedling trays…

Soil is kept too wet – Solution: Water seedlings from the bottom so the top of the soil can dry out a bit between waterings (potting up seedlings will make it easier to control the soil moisture level, and get rid of soil gnats). Store all unused seed starting soil in a air-tight container. Hang yellow sticky traps near your seedlings to help control the adult soil gnats.

Yellow sticky trap controls soil gnats in seed trays

Yellow sticky trap controls soil gnats in seed trays

Tips for growing strong healthy seedlings

The best advice I can offer you to help with seedlings is to try your best to prevent problems from happening in the first place. Many of these are fixable, but some seedlings can’t be saved and you’ll have to start all over from scratch (ugh!). The good news is that it’s not difficult to care for seedlings, and there are only a few key things to remember.

  • Sterilize all of your seed starting supplies and equipment every time you use them
  • Always use a good quality seed starting potting soil
  • Keep seedling soil consistently moist, but never soggy
  • Water seedling trays from the bottom rather than the top
  • Get some seed starting grow lights, and always give seedlings the proper amount of light
  • Ensure adequate ventilation and airflow around your seedlings
Strong healthy seedlings ready to be transplanted

Strong healthy seedlings ready to be transplanted

Remember, don’t feel bad if you’ve experienced any (or all) of these problems, we’ve all been there. It’s best to avoid them all together, and prevention is the most important step you can take. The best part is, once you get the hang of it, you’ll be able to grow healthy seedlings indoors without any problems at all. But of course, if you need more help with seedlings, we’re always here for you!

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What advice would you give to give to people who need help with seedlings? Share your tips in the comments section below.

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Figure out why your seedlings are struggling (or worse, falling over and dying), and get help with seedlings in this comprehensive troubleshooting guide.



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