Common Seed Starting Problems (and Solutions!)

Learn about the common seed starting problems that can happen when you start seeds inside. I’ll go over the most common seed starting problems and give you practical solutions for them. I’ll also go over a few specific seed starting problem scenarios and solutions to those as well. This article will give you thorough and highly-detailed tips on having as much success as possible when you start seeds inside.

Common Seed Starting Problems and Solutions

Common Seed Starting Problems (and Solutions)

Now that I’ve shown you how to properly start seeds inside, let’s go over some of the most common seed starting problems (and solutions!) that can come up from this gardening experience.

If you are too lazy/tired to read a lot today, I’ll tell you the main culprits for seed starting problems in this one sentence: the MOST common problems for seed starting include overwatering, not enough light, and incorrect soil temperatures.

Let’s take a close look at the most common seed starting problems and what you can do about them.

Common Seed Starting Problems and Solutions

Common Seed Starting Problems #1: Damping Off

What is Damping Off?

Damping off is a common soil-born fungal disease that affects seedlings. It can be caused by many types of fungal diseases, including several root rots and molds. The ‘damping off’ term is used to describe the sudden death of tender seedlings. The most common way to know you had damping off issues is when a seedling looks healthy one day and completely withers and dies the next day. Sometimes the seedlings look like they have been pinched at the soil line.

What Causes Damping Off?

Damping off is caused by fungus that thrives in environments with excessive moisture and/or poor air circulation.

Can You Treat Seedlings with Damping Off Symptoms?

Sadly, there is no cure for plants that already have damping off symptoms. Besides prevention (tips below), you should try to stop the damping off from spreading to your other seedlings.

Here are some ways to prevent your other seedlings from dying from damping off:

  • When a seedling dies from damping off, immediately remove it from the area to prevent the spread of the disease.
  • If you see white or green mold on the soil surface of other seedlings, lightly scratch up the soil to increase aeration.
  • Stop overwatering: overwatering encourages damping off issues.
  • Sprinkle cinnamon over the soil surface to inhibit the growth of the damping off fungus.
  • Have a fan gently blowing on your seedlings to help with air circulation.

How Can You Prevent Damping Off?

You can prevent future damping off issues with the following tips:

  1. Use sterilized homemade potting soil OR organic seed starter mix to give your seeds a healthy start.
  2. If you are reusing containers, make sure they are clean. Here’s a great tutorial on disinfecting seed trays.
  3. Fill the seed containers with dirt up to the brim and plant seeds close to the soil surface so that your seeds get proper air circulation.
  4. Don’t overcrowd your containers. Sow thinly so each plant has proper air circulation.
  5. Give your seedlings proper heat (with a heating mat) and light (with at least 12 hours of light) to ensure the growth of healthy plants.
  6. Consider using seed trays and provide water from the bottom instead of doing overhead watering.
  7. DO NOT overwater your seeds and seedlings.

Common Seed Starting Problems and Solutions

Common Seed Starting Problems #2: Legginess

What is Legginess?

Leggy plants have thin, weak stems and they often have large gaps between leaves. Leggy plants are tall and spindly, and are often found bent over in half, because the top of the plants is too heavy for the stems to hold up.

What Causes Legginess in Plants?

Legginess is caused by plants not receiving enough light. Seedlings need around 12-16 hours of light each day. Usually, sunlight from your window is not enough to prevent legginess. You should consider getting a plant lighting system (you can easily make one or buy a lighting system like this), and keep the lights 2 inches above the seedlings for optimal growth.

Leggy plants are also a result from overcrowding, as the seedlings compete with each other for optimal lighting.

Can You Treat Seedlings with Legginess Symptoms?

If you catch the legginess quick enough, there are a few things you can do to try to save the plants:

  • Rotate your seed trays. If you are trying to use only light from a window, rotate the seed trays a few times a day to give all of your seedlings equal time closest to the light from the window. This can help with over-competition between the plants for the most light, which causes legginess.
  • Whenever possible, put your seed trays outside. If you are trying to use only light from a window, take advantage of warm, sunny days and put your seedlings outside in a protected area for a few hours. The direct sunlight can be greatly beneficial for them and can help them with the upcoming transplanting process. NOTE: Start this process gradually or you can give your plants transplant shock or sunburn.
  • Thin your seedlings. Overcrowded plants compete for the light, which can make them leggy. Thin your seedlings to the strongest, healthiest plant per pot.
  • Transplant your leggy seedlings. Gently transplant your seedlings into new pots with new soil, and gently bury as much of the leggy part of the seedling as possible. This won’t always work, but it’s worth a try to save your plant. The important key is to be gentle and try not the ruin their roots.
  • Use a grow light. If you are dealing with leggy seedlings, chances are, you aren’t using a grow light. A grow light is the easiest way to both fix and prevent legginess.

How Can You Prevent Legginess?

Legginess is very easy to prevent:

  • Use an adjustable grow light and place it 2-3 inches above the plants. This prevents the seedlings from reaching out for more light.
  • Avoid overcrowding the pots. Overcrowded plants compete for light and become leggy.
  • Consider having a fan gently blowing on your seedlings. Wind can help make sturdy, thick stems on your seedlings, so stimulate wind with a fan.

Common Seed Starting Problems and Solutions

Common Seed Starting Problems #3: Indoor Pests

What type of indoor pests can affect my seedlings?

Fungus gnats (which are similar to fruit flies) and aphids are the most common indoor pest problem with seedlings. Since there are no natural predators inside your home, you need to both watch closely for pests and act quickly when you see them.

Can You Treat Seedlings with Indoor Pest Problems?

If your seedlings are big and hearty enough, you can gently wash them with a mild soapy water to get rid of aphids. Learn more about treating seedlings for aphids in this article from The Spruce.

For fungus gnats, you can sprinkle the top of the soil of the seedlings with either cinnamon and/or sand. Cinnamon destroys the fungus that the gnat larvae feeds on, and sand makes the gnats think the soil is too dry to place their eggs. Learn more about fighting against indoor fungus gnats in this article from Small Footprint Family.

How Can You Prevent Problems with Indoor Pests?

The best ways to prevent problems with indoor pests includes:

  • Do NOT overwater! Indoor pest problems are most likely if you are overwatering. Pests love soggy, wet soil.
  • Disinfect seed trays. At the very least, spray out your seed trays each year with hot water. Use a safe, organic mild soap as well if you are having constant pest problems (or fungus problems).
  • Work on improving the air flow. Good air flow prevents soggy soil and fungus problems, both of which attract the pests. Consider getting a fan to gently blow on your seedlings.

Common Seed Starting Problems and Solutions

Specific Seed Starting Questions (and Solutions)

If you’re not sure what the problem is with your seedlings, I’ve added a few scenarios below as well as the solutions to these specific circumstances. Feel free to add your specific scenario questions about seed starting troubles in the comments below and I’ll add them to this list and figure out some answers for you!

Specific Scenario #1: Why Didn’t My Seeds Germinate?

The most common reasons why your seeds didn’t germinate (aka they didn’t even start growing) include:

  • They were old seeds. If you properly store your seeds in a dark, cool, and dry location, your seeds can last for around 3-5 years. However, the older the seeds get, the lower the germination rate. Click here to learn how to test your old seeds for viability.
  • Wrong temperature for the soil. Most vegetable plants require a soil temperature of around 65-75 degrees Fahrenheit to germinate. However, cold weather crops like cabbage and broccoli need a cooler soil temperature. Also, many herbs and flowers have specific soil temperatures needed for germination.  For your spring/summer vegetable plants, consider getting a seed heating mat. For cold weather crops, herbs, and flowers, research the specific needs of those specific plants.
  • You planted your seeds either too shallow or too deep. Make sure you read the seed packets for the correct soil depth for the seeds. Some seeds need to be scattered on top of the soil because they need light in order to germinate; and other seeds need to be placed under the soil in order to prevent drying out.
  • You are not watering properly. In the germination stage, you need to keep the soil evenly moist. If you overwater the soil, the seeds might rot before they germinate, however, seeds also cannot germinate if you let the soil get too dry. Figuring out the perfect balance in watering is a skill that comes with practice and experimentation.


Specific Scenario #2: Why Did My Seedlings Stop Growing?

If your seedlings are alive and just stopped growing bigger, here are a few reasons why that might have happened:

  • There is a nutrient deficiency problem with your soil. Seed starting soil do not contain many nutrients. If you are growing your seedlings indoors for more than a few weeks, you should consider giving them a nutrient boost. An organic fertilizer would be best and give it in a low dose (at LEAST half of what you would give it outdoors), something like organic kelp seaweed fertilizer or organic fish fertilizer will work.
  • You have cold soil temperatures. If your soil temperatures are cool (aka you aren’t using a seed heating mat), you will see slower growth for your plants. Warm weather crops, including peppers and tomatoes, need warm soil temperatures to grow well. If the reason they stopped growing is cold soil, then they should start growing again when their soil is at least 70 degrees fahrenheit.
  • You have been overwatering your plants. Overwatering is one of the big reasons for stunted growth. If your seedlings stop growing and start showing yellow tips on their leaves, it is probably because of overwatering.


Specific Scenario #3: Why Did My Seeds Sprout and Then Suddenly Die?

If your plant looks happy and healthy one day and then withers and die the next day, you most likely have damping off problems. Check out the tips located above in Common Problem #1.

Common Seed Starting Problems…Ask Me For Help!

I hope this article on common seed starting problems and solutions helped you feel more confident about starting seeds inside. Make sure you check out my thorough article on How to Start Seeds Inside for more tips!

I love helping my readers figure out their gardening problems, so if you have more questions about seed starting issues, please comment below and I’ll try to figure out some answers for you!

More Gardening Tips:


Common Seed Starting Problems and Solutions




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