Troubleshooting Seedling Problems

Two of the most common seedling problems are described below. Learn how to identify the issue, fix the problem, and prevent the issue from happening again in the future.

Problem #1: My seeds germinated but are not growing taller

If seedlings germinate and emerge but do not grow past a few inches tall, start with reviewing the growing conditions. Newly emerged seedlings prefer bright overhead light, warm temperatures, and even moisture.

If growing in germination trays, remove any tray covers that may be covering the seedlings.
If seedlings are thin and weak, provide supplemental light or adjust lighting so that it is directly above the seedlings.
Monitor soil moisture and water as needed to maintain even moisture. Soil should not be soaking wet or extremely dry. Allow soil to dry slightly between watering to encourage strong root growth. If algae growth appears on the soil surface, reduce frequency of watering.
Many seed starting mixes contain only small amounts of soil nutrients. When seedlings reach a few inches tall and have developed true leaves, it is a good time to fertilize them with a low-strength water-soluble fertilizer. For many vegetable and flower species, once per week is an adequate fertilization schedule.
Healthy seedlings can outgrow germination cell trays quickly. If the soil is drying down quickly and the seedlings seem to be growing more slowly, it may be time to transplant them into a larger container. A seedling that has outgrown its cell will have dense white roots easily visible when lifted from the cell tray or sometimes growing through the bottom of the tray. Transplant these root-bound seedlings to a larger container or to their final garden bed as soon as possible to reduce stress and prevent stunting.

Problem #2: My seeds germinated but died shortly after

If seedlings emerge and die shortly after or they reach a few inches tall and then die, it is possible they were killed by Damping off, a seedling disease. Damping off occurs when seedlings are overwatered and a fungus or mold infects the trays, killing the vulnerable seedlings. The smaller the seedling is, the more susceptible it will be to the disease.

Symptoms of Damping off include:

Failure of seedlings to emerge from the soil.
Seedling stems and cotyledons are water-soaked, mushy, and discolored.
Young leaves wilt and turn gray to brown.
Roots are absent, stunted, or discolored.
White mold is visible on infected plant parts or soil.

Damping off is caused by a fungus or mold (often Fusarium spp., Rhizoctonia spp. or Pythium spp.) that thrive in cool, wet conditions and are spread easily by contaminated tools, pots, trays, and potting soil. They can also be carried by irrigation splash and certain insects, like fungus gnats. It is common for Damping off to kill large sections or whole trays of seedlings, or to cause root or crown rot in more mature plants.

To prevent Damping off:

Sterilize all used pots, trays, and tools with a solution of 10% bleach prior to use.
Use new potting soil for starting seedlings. Do not re-use soil or use garden soil or compost.
Avoid overwatering and choose pots and trays with good drainage holes.
Keep soil temperatures warm with a heat mat and water seedlings with clean warm water.
Keep seedlings healthy by providing bright overhead light, warm temperatures, and even soil moisture.