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Common Seedling Problems

While producing seedlings indoor can be a truly reinvigorating activity, especially for those of us who as still dealing with the last throes of winter, it can quickly become thoroughly exhausting when things don’t turn out as planned. Here are a few problems you may encounter, how to identify and deal with them.

Damping-Off

Seedlings fall over and appear water-soaked at the base of the stem. The affected area might look slimy or mushy. Seedlings might die before or shortly after emerging.

Photo: Bre jaye.

Leggy Seedlings

Seedlings have unusually long stems, often weak and thin, struggling to stand upright. They may lean towards a light source if it’s not directly overhead.

Leaf Discoloration (Yellowing or Browning)

Yellowing often starts with the older, lower leaves. It can indicate overwatering, underwatering, or nutrient deficiencies (commonly nitrogen). Tips or edges of leaves can turn brown.

Wilting

Leaves droop, look limp, and the plant loses its rigidity. Wilting can occur with both dry and waterlogged soils.

Pest Infestations

Visible insects or mites on the plant, under leaves, or on the soil. Look for honeydew (sticky residue), webbing, or leaf damage like holes, spots, or chewed edges.

Photo: Photo: Gerro, jardins-du-nord.fr.

Mold or Fungus on Soil

White, green, or black mold growth on the soil surface. You may also notice a musty smell.

Leaf Spot Diseases

Circular or irregular-shaped spots on leaves, which may be brown, black, yellow, or red. The center of the spot might fall out, leaving a hole.

Photo: Scot Nelson.

Nutrient Burn

Leaf tips and edges turn brown or black and appear burned. This problem often starts with the lower leaves and moves upward.

Temperature Stress

Too Cold: Stunted growth, purpling of leaves or stems, wilting.

Too Hot: Leaves curl upwards, dry out, or show signs of sunburn (bleached spots).

Managing these issues often involves a balance of preventative measures and timely interventions. Regular monitoring and adapting to the needs of your seedlings as they grow will help ensure their healthy development.

Excess Light

Intense artificial sources or prolonged direct sunlight can lead to stress and growth issues in seedlings, evident through signs like leaf scorching, fading or bleaching, and wilting.

Purple Leaves

Seedlings displaying purple leaves and stems, often on the underside or along the veins, accompanied by slowed or stunted growth.


Prevention is key! Use sterile potting mix and containers and ensure good drainage and air circulation. Provide sufficient light, monitor water intake and apply balanced, mild fertilizers to prevent nutrient imbalances. Inspect regularly for pests and diseases. Be careful of any sudden changes in the seedlings environment which could cause them stress. Relax and enjoy, though you may run into problems, you can always try again or buy seedlings from a garden center when all else fails!

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