Most Common Seed Starting Problems- and How to Fix Them

seed starting problems

Seed starting can be a tricky process. It’s not always as simple as sticking a seed in some soil and giving it a little water. Below you will find the 4 most common seed starting problems- as well as some ways to fix or prevent them!

The most common seed starting problems are:

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My seeds never germinate!


Germination problems can be caused by a variety of reasons. Some of the most common are:

seed starting problems

  • Incorrect Temperature. Different seeds have different needs. Cool weather crops such as cabbage, kale or broccoli have a much lower germination temperature while warm weather crops like tomatoes will germinate better with temperatures in the 70F range. If you are sprouting your seeds in a cool basement or outbuilding you may need to provide supplemental heat- such as a heating mat– to ensure germination.
  • Old Seeds. When properly stored seeds can have a very long shelf life. But the older they get, your germination rate will begin to reduce. For the longest life, store your seeds in a cold, dry place. Humidity and warmth will greatly reduce your seeds’ shelf life.
  • Incorrect Watering. Water in a necessity for all plants. In the germination stage you need to make sure you keep the soil evenly moist. If you water too much, you run the risk of your seeds rotting before they germinate. If you let them dry out, they will either never germinate or die trying!
  • Planting Depth/Light. When you plant your seeds pay attention to your planting depth. This is important because if planted too deep you plants could run out of energy before reaching sunlight. Planting too shallow can lead to drying out. Some seeds actually need some light to germinate, so instead of digging them down you just press them into your soil. Read your seed packets for information on each seed.

My seeds sprout and then die!


Everything starts off good. Your seeds germinate and you have little seedlings growing strong. Then all of a sudden they whither up and die! This is often called “dampening off”. It can be prevented by using these seed starting practices:

seed starting problems

  • Do not over water. Too much moisture allows disease to grow and plants to mold. Once your seeds have germinated, water your seedlings only when the soil is beginning to dry out. Watering from the bottom is best, but do not allow them to sit in standing water once they are done taking it in.
  • Do not overcrowd. Your plants need room to breathe. A room with good airflow, as well as enough space between the plants will help them stay healthy.
  • Start with clean soil. Oftentimes disease in seedlings is caused by disease that is laying dormant in your soil or in your seed starting pots. Wash your seed pots and trays each year before planting. Consider buying a sterile soil if you have a major problem, that is not cured by the already mentioned steps.


It all started off good, but my seedlings just aren’t getting very big!


They sprouted, they are alive, but they just aren’t growing!! Just like with germination, different seeds have different needs. But here are some of the common reasons for stunted growth in your seedlings:

seed starting problems

  • Incorrect temperature. If it is very cold your seedlings will not grow at the same rate they would in warm weather. Warm weather crops like peppers, tomatoes, or eggplant require temperatures around 75F to be happy. Even if they are small chances are when it warms up and they are outdoors they will take off and make up for their slow start.
  • Nutrient deficiencies. If you seed starting medium is lacking in nutrients they will not grow properly. Keep an eye out for the symptoms of some common soil nutrient deficiencies and feed your plants a little bit as they grow.
  • Overwatering. Overwatering is the number one cause of stunted growth. If your seedlings are stunted and have yellow tips, this is most likely the cause. Waterlogged soil prevents the plant’s roots from bringing in oxygen, which will damage the roots and the seedling will be at risk for many more problems. Let the soil dry out just a bit before watering- and the soil should be moist not soaked.


My seedlings are tall, thin and leggy!

Legginess is a common problem in plants that are started indoors and it is caused by the seedlings having to compete and stretch for their light source. Here are a couple of ways to reduce the tall, leggy appearance of your seedlings:

seed starting problems

  • Rotate your trays. If you are using a south facing window, make sure to rotate your plants a couple of times a day so that all plants have an equal time closest to the window. Even if you are using an artificial grow light, rotating the plants within your trays is still a good idea so that all get equal time directly under the light.
  • Take advantage of warm, sunny days. If you have a warm day, set your seedlings outside in a protected area for a few hours. They will benefit from the direct sunlight, as well as get a headstart on the hardening off process.
  • Use a grow light in addition to your sunny window to ensure the optimum daylight length of 15-18 hours.
  • Thin out your seedlings. The more crowded they are, the more they will have to compete for light.


Those are the top 4, most common seed starting problems, what do you have the most trouble with when it comes to seed starting?



© 2014 – 2016, Sarah R Toney. All rights reserved.

13 comments on “Most Common Seed Starting Problems- and How to Fix Them

  1. Charlene Carswell says:

    Enjoyed reading your info re: plants /growing info

  2. Little Sis says:

    I know I’ve watered too much in the past, but I didn’t understand why it was SUCH a problem. Perhaps I can stay my hand now. Thanks!

  3. Monica says:

    I just started my seeds last week, and finally have some cute little seedlings. I’m always so scared if they will make it or not! Last year I didn’t have such good luck, but I’m a little wiser this year. Thanks for the extra tips to make sure I get some nice, strong plants!

  4. Lila says:

    Thanks for these sage tips! We have some leggy radishes right now that could definitely use to be thinned…now, to find the time!

  5. […] I talked about the common seed starting problems, I mentioned that poor germination was often a result of incorrect planting depth. This is because […]

  6. christine says:

    Do you fertilize? I am trying organic seeds, want to use fish emulsion, but don’t know when to start. Thanks

    • I don’t fertilize unless there seems to be a need for it. I do like to water with water from my fish tanks, which adds some nutrients. They don’t need much in the way of nutrients when they are germinating or as sprouts- I am sure it wouldn’t hurt once they have a couple of true leaves

  7. Hannah says:

    My worst problem used to be ‘damping off’, but now I water from the bottom the first few times with (cool) chamomile tea.

  8. […] Common Seed Starting Problems and How to Fix Them […]

  9. winnie says:

    What causes my soil to get moldy when starting my seeds indoors?

  10. Margaret says:

    I started a lot of impatients and wave petunia seeds this year. Also lemon grass and Hostas in newspaper pots with potting soil. I placed them in a seed starting pan with a lid. They were kept moist, under grow lights, and afternoon sun. Most of them germinated but never grew after they came through the soil. They lived that way for a couple months. I talked to the seed company and they sent more seeds. It is a very reputable seed business so I am sure that it is not the seeds. I replanted altho it was May by then. Same thing. I put these outdoors when they came through the soil. Its July and they are still there, same size, little 2 leaf starts nothing more. I am stumped by this and I have no idea what I have wrong. I have gardened a grown house plants for years without a problem…..ideas????

  11. Ken says:

    Did you use new potting soil? or re-use the old stuff? It sounds like you are in a cycle that repeats itself so….. something in your method needs to change, eh? Sending more seeds is the only thing a seed co. can do, and kudos to whomever it is, but they can’t solve your problem because when they grow their seeds, they have a proven method they use time after time. You have to find your own proven method…does this make sense to you.

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