Troubleshooting Seed and Seedling Problems

, written by Benedict Vanheems gb flag

Seedlings on a windowsill

Ready…set…sow! If you haven’t got your first seedlings underway now’s the time to think about getting started. Actually, scratch that: less thinking, more doing! Depending on where you live the growing season has either already begun or is just about to, so there’s no time to waste!

Hopefully your sowing schedule will get off to a strong start but to help you on your way I’ve put together a few pointers for diagnosing and troubleshooting some of the most common problems associated with germination and young seedlings.

Germination Problems

What, no seedlings? Don’t worry, we’ve all fallen at the first hurdle. There are several reasons why seeds fail to germinate, so let’s take each in turn.

Old seed: Like fresh food, seeds have a use-by date. Check seed packets and, if in doubt, try a simple germination test to ascertain once and for all whether seeds are good for sowing or throwing. Seeds of some vegetables, like parsnip and onion, only keep for one year, while others will store well for up to five years or even longer. How you store seed has a profound effect on its viability too.

Perform a germination test if you believe seeds may be past their best

Timing: I’ve said it so many times before I’m at risk of boring you to tears but it’s worth repeating (again!): patience is a virtue. Sometimes seedlings fail to appear because they simply haven’t had enough time to do so! Check seed packets for typical germination times but bear in mind these reflect ideal conditions. Case in point: radishes are notorious for speed but it took three weeks for seedlings to emerge from a recent sowing in my unheated greenhouse. Vegetables known for slow germination can be chivvied along by pre-sprouting on damp paper towel before carefully planting the tiny seedlings.

Temperature: Different seeds need different temperatures. Cool-season crops like lettuce or any of the brassicas happily germinate at temperatures as low as 10°C (50°F), while warm-season vegetables prefer something above 20°C (68°F). Refer to seed packets and check the temperature at soil level to ensure seeds are cosseted correctly. Heat mats and propagators help to raise the temperature and keep it steady, while a cool cellar, cloak of damp newspaper or overhang of shade cloth should counter hot weather.

Moisture: If seeds are too wet they run the risk of rotting before they’ve had a chance to germinate, but too dry and seeds won’t receive the cue to sprout. I like to moisten my seed sowing mix before sowing, using a spray bottle to dampen the mix before using it to fill containers.

Pots of warm-season favorites like peppers and tomatoes germinate quicker when covered with a propagator lid or clear plastic, which raises humidity to the steamy level they love. Remove covers once the seedlings are up.

Starting tomatoes and peppers under a propagator lid increases humidity

Damping Off

Your seedlings are up but then they collapse and wither as quickly as they appeared. It’s a common complaint, and ‘damping off’ is the culprit. Damping off is caused by one of a number of soil or water-borne fungi that thrive in very wet and/or muggy conditions. Seedlings typically collapse at the base and sometimes you may notice fluffy white fungal growth spreading across the soil surface. Attacks spread with alarming speed.

The solution is to ensure good air circulation at all times, while taking care not to overwater. Always use clean pots and trays and fresh seed starting mix, and water seedlings with mains water, not rainwater that’s been standing around.

Moldy potting soil is a sign of overly wet conditions

Moldy Potting Soil

Green or white mold across the soil surface is unlikely to harm seedlings in itself but is a sign that conditions at the root zone are too wet. Consider it a warning and react accordingly.

Begin by gently scraping off the mold then improve air circulation around seedlings, for example by opening up all vents in the greenhouse. Surface mold is less likely to develop when seedlings are watered from below. Sit pots and trays in a reservoir of water until you can see moisture at the surface. Remove them immediately and insure that any excess moisture can drain out freely from the bottom.

Fungus Gnats

The barely discernible flies flitting about just above soil level are probably fungus gnats. While the adult flies don’t damage plants, their larvae can, feeding at the roots so that seedlings fail to flourish.

Tiny flies may be fungus gnats, whose larvae feed on plant roots

If you spot fungus gnats you have a few tactics at your disposal. First, allow seedlings to dry out slightly between waterings. Newly sown pots can be covered until they have germinated to deny gnats access. Hanging up yellow sticky traps, horizontally and close to soil level, is an effective way to put a dent in fungus gnat numbers. Good hygiene in and around propagation areas goes a long way to avoiding problems in the first place.

Leggy Seedlings

Stretched seedlings with big gaps between sets of leaves and an often pale complexion are classic signs of poor light levels. They can also be symptoms of overcrowding or excess heat. Each of these causes is easily rectified.

To address a lack of light, often accompanied by seedlings leaning towards a light source, move seedlings onto a brighter windowsill or consider setting up grow lights early on in the season.

Seedlings that don’t receive enough light become stretched out

The alternative is to just wait another week or two for conditions to warm up enough to begin sowing in the greenhouse or directly outdoors. Good airflow will help to keep greenhouse highs pegged to something a little less exhausting, while sowing with restraint and prompt thinning will prevent problems with overcrowding.

These are the most common problems associated with germination as experienced by myself and others in the GrowVeg team. Barbara Pleasant offers plenty more in her article on starting seeds indoors indoors and don’t forget to check out our pest and disease identification guides for other culprits. Forewarned is forearmed!

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Show Comments


"Ihave noticed since keeping my own runner bean seeds there have been quite a number of seeds with brown blotches on. What I would like to know is should I disgard them and throw them away, or plant them next year as normal. "
Raymond Bowcott on Friday 11 October 2019
"If the seeds are still firm and intact then I would continue to save them. However, if you have lots of seeds to spare then it may be prudent to discard any with brown blotches and just save those that are more typical of what you would expect to save - just in case!"
Ben Vanheems on Monday 14 October 2019
"I have some tomato seedlings that just came out of a propagator lid and are under indoor light. on day two the leaves are turning white and brownish yellow on the tips. what do you think could be wrong???"
Frank on Wednesday 1 April 2020
"Hi Frank. That's a tricky one. Are they getting enough light for a start? They need at least 12 hours of good light, and anywhere up to 16. Could the lights be too close to the seedling leaves? This could make the area around the leaves too hot, leading to scorching."
Ben Vanheems on Thursday 2 April 2020
"I planted single tomato seeds in a small divided container and some are coming up with double or even triple stems. Why is this and what should I do about it?"
Amanda Jeffries on Wednesday 8 April 2020
"Hi Amanda. I have to say that is a mystery. Were they definitely tomato seeds and not something like beets/beetroot, which can often produce two or three seedlings per 'seed'?"
Ben Vanheems on Thursday 9 April 2020
"I have been growing Suttons "Crimson Crush" seeds for several years, However, last year and this hardly any of my Sutton seeds germinated, whereas similar seeds, planted at the same time and in a similar manner and in the same place, nearly all (circa 95% or more) all produced young plants. These other seeds were partly ones purchased from Premier Seeds and the others were seeds saved from my Crimson Crush tomato crop of three years ago, which were still successfully planted this year. The latter, won't grow exactly true to original, as they were from F1 seeds, but I saw little difference in those planted last year."
John on Sunday 3 April 2022
"Hi Amanda, love your website! I have planted a seed from a persimmon stone (in winter), placed in a warm, completely dark room and, as nothing happened for many many weeks, totally forgot about it. To my surprise I now discovered it has germinated into an 11 cm long, pale looking young plant! What should I do? How much water and sun can I expose it to, after these harsh conditions? Go slow, go fast? Soil was completely dry, no sunlight.. "
Helga on Friday 12 August 2022

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