Vegetable Seed and Seedling Problems


Successful seed and seedlings growth depend on moisture, warmth, air, and light. Seeds and seedlings, as well, require optimal temperatures, even watering, open air circulation, and bright light to thrive.

When vegetable seeds fail to sprout or when seedlings wither and die what could the problem be? Often the answer is simple.

Seeds Fail to Sprout. The cause is likely one of these:

Temperature is too low or too high. Check the seed packet for the seed’s optimal germination temperature. Most vegetable seeds prefer soil temperatures between 70° and 80°F for germination.

Soil was allowed to dry out. Seeds must absorb moisture to begin germination. The seed coat expands with water and allows the embryo to begin growth.

Seeds planted to deep. As a rule of thumb do not plant seeds greater than the width of their diameter; this if often just ¼ to ½ inch deep and sometimes less. Most seeds require light to germinate.

Too much water. Watering caused seeds sown just below the soil surface to become exposed and float away. Dampen the soil before you sow seed then be careful not to overwater after sowing.

Insufficient soil contact. Seed coats are tough. Beneficial bacteria and fungi in the soil along with moisture help break down the seed coat and allow germination and growth to begin. Gently press down on the soil after you sow seed to make sure the seed and soil come in contact.

Poor soil. The best soil is half solid matter and half pore space–the pore space contains air and water. Clay soil is flat with no space for air. Sandy soil is too loose and does not hold moisture well. The best soil should be rich in decomposed organic matter or compost; this soil will have just what seeds and seedlings need. If you suspect the soil is poor, amend the soil with aged compost and re-sow.

Damping-off disease. Damping-off is a fungal disease that can attack just germinated plants. Damping-off is often a sign that the soil is too moist or to rich in nutrients. Use a sterile seed starting medium.

Light and dark. Most seeds require light to germinate; some seeds require darkness. Seeds are light sensitive. Germination often depends on exposure to red light waves–even through soil cover. Check seed packets or grower’s guides to see if special light conditions must be present for germination.

Seedling Problems

Once seeds have sprouted and begun to grow keep the soil just moist–do not overwater or allow the soil to dry out, provide strong light–14 to 16 hours each day–and good air circulation, and avoid over-feeding.

Here are common seedling problems and responses:

Leaf Curl. Too much fertilizer will cause leaves to curl, especially in bright light. Decrease the amount of fertilizer and if the problem is severe replant the seedling in fresh potting soil.

Yellow Lower Leaves. Too much fertilizer can cause leaves to yellow. Avoid over feeding young plants. Make sure there is good air circulation around the plants.

Leggy Plants. A leggy plant has large gaps or spaces between leaves and thin, weak stems. Be sure the plant is getting sufficient light. Don’t let the temperature get too high. Make sure your plants are not overcrowded. A good course of action is to transplant the leggy plant into a deeper container.

Leaf Discoloration. Off-colored leaves are often a sign of nutrient deficiency. Pale leaves may be a sign of nitrogen deficiency or lack of enough light. Deep purple veining can indicate a deficiency in nitrogen. Reddish purple undersides can be a sign of phosphorus deficiency; the seedling may also be stunted with thin, fibrous stems. When the soil is too acid, phosphorus is not taken up from the soil. Bronze or brown leaf edges can be a sign of potassium deficiency or overwatering.

When leaf discoloration occurs, repot the seedling into a medium that contains compost. Compost is likely to contain the trace minerals plants need.

Discolored Roots. Discolored roots can be caused by overfeeding or overheating which can result in excess fertilizer salts being released into the soil. Replant the seedlings in fresh soil or leach away the toxic salts. Use well aerated soil and do not overfeed or overwater.

Mold. Mold on the soil surface is a sign of poor drainage and lack of air circulation. Scratch the soil to increase aeration, move seedlings to a place with good air circulation. You can also add powdered charcoal to the soil surface.

Insect Damage. Indentify the insect at work. Prevention is always the best course of action. Avoid overfeeding which can result in excessive green growth which can attract insects such as aphids. Keep the greenhouse or garden free of plant debris which can harbor sowbugs, slugs, and snails. Place plants where there is good air circulation to slow down spider mites. Use yellow sticky traps to control whiteflies. Knock insects off plants with a strong stream of water.

Damping-off. Withered seedlings and plant failure is a sign of the fungal disease damping-off. Damping-off attacks plant stems at the soil surface. Too much nitrogen and moisture can result in damping-off. Too little air circulation can also lead to damping-off. Prevention is the only course of action: maintain good air circulation, avoid overwatering, sow seeds in a sterile medium, and pre-soak seeds in water with a tablespoon of clove oil or crushed garlic cloves added–these have anti-fungal properties.

Poor Root Growth. If transplants fail to root well then several factors may be at play: poorly drained soil, insufficient soil fertility, over-fertilization, the temperature is too low, seed starting medium or soil insufficiently aerated. Repot the seedling is sterile potting mix and protect the seedling from broad swings in temperature. Keep the soil mix just moist.

Written by Stephen Albert

Stephen Albert is a horticulturist, master gardener, and certified nurseryman who has taught at the University of California for more than 25 years. He holds graduate degrees from the University of California and the University of Iowa. His books include Vegetable Garden Grower’s Guide, Vegetable Garden Almanac & Planner, Tomato Grower’s Answer Book, and Kitchen Garden Grower’s Guide. His Vegetable Garden Grower’s Masterclass is available online. has more than 10 million visitors each year.


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  1. hi there just wondering my seed germinated the top is resting on the soil will it raise its head the other seed grew straight no issues

    • If an emerging seedling does not grow up to the light give it a day or two particularly if the weather is hot or chilly. If the seedling does not grow up within a couple of days it may have been attacked by the damping off fungus. Keep seed starting mix or soil just lightly moist and give seedlings at least 10 hours of light each day; an air temperature of 70-75F is optimal.

    • Quinoa is a grain-like crop native to the Andes in South America. It is commonly grown at altitude but some varieties grow in coastal regions. The optimal growing conditions for quiona are in cool climates with temperatures that range from 25°F/−3°C, during the night, to near 95°F/35°C, during the day. You may not get weather warm enough in Forestville, though I would encourage you to give it a try. Keep the soil evenly moist during early growth and development, as harvest nears quinoa likes soil on the dry side.

  2. Your articles are great. Thanks for the information on leggy vegetables and the fact they can be buried up to their bottom leaves. I knew I could do that to tomatoes but not brussle sprouts. I also thought your info on seedlings was very helpful.

    Thanks again

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