Troubleshooting Seed Starting Problems: Leggy Seedlings, Damping Off, Weak Growth, and More

ByStephen Albert

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Starting seeds indoors is one of my favorite parts of the gardening year. After more than 30 years of raising vegetables from seed—on heat mats, under lights, in greenhouses, and in my Sonoma Valley kitchen—I’ve run into every problem imaginable. Fortunately, most seed-starting issues are easy to diagnose and fix once you know what to look for.

Below are the most common problems gardeners face—leggy seedlings, damping off, and weak, slow growth—and the practical solutions I’ve come to rely on.

Leggy Seedlings

Leggy seedlings have long, thin, stretched stems and often lean toward the nearest window or light source.

Why It Happens

  • Not enough light or light placed too far from seedlings
  • Excess heat without enough light
  • Overcrowded seedlings competing for light

Fixes That Work

• Lower your grow lights.
Keep fluorescent or LED lights 2–4 inches above seedling tops. Raise them as seedlings grow.

• Increase daily light time.
Give seedlings 14–16 hours of bright light each day. A timer makes this foolproof.

• Reduce heat after germination.
I start seeds warm (70–75°F), then drop to 60–65°F after sprouts appear to prevent stretching.

• Thin crowded seedlings.
I’ve learned not to hesitate—thin to one strong plant per cell to prevent competition.

Damping Off

Damping off is a fungal disease that causes seedlings to collapse at the soil line. Once it hits, the affected seedlings cannot be saved—but you can prevent it.

Why It Happens

  • Soil too wet or poor ventilation
  • Contaminated containers or old seed trays
  • Heavy, non-sterile garden soil used indoors

Fixes That Work

• Start with sterile seed-starting mix.
This prevents fungal spores from ever becoming a problem.

• Water from the bottom.
I set trays in a shallow pan of water for a few minutes. This keeps stems dry—your best defense.

• Improve air circulation.
Run a small fan on low. It keeps stems strong and reduces fungal pressure.

• Don’t overwater.
Let the top of the soil dry slightly between waterings. Seedlings need moisture—not soggy soil.

• Clean trays yearly.
I soak mine in hot water with a splash of hydrogen peroxide.

Weak or Slow Growth

Sometimes seedlings look healthy but just… don’t grow. This usually means their basic needs aren’t being met.

Why It Happens

  • Not enough light
  • Lack of nutrients after the first true leaves
  • Soil too cold
  • Containers too small or roots crowded

Fixes That Work

• Boost the light.
Weak growth is almost always a light problem. Add another fixture or lower existing lights.

• Feed lightly.
Once seedlings have their first true leaves, I feed with half-strength organic liquid fertilizer every 10–14 days.

• Warm the soil.
Peppers, tomatoes, and eggplants grow noticeably faster with 70–75°F soil.

• Pot up on time.
If roots circle the cell, it’s time to transplant to a larger container.

My Seed Starting Golden Rules

These are the practices that have consistently given me strong seedlings year after year:

  • Provide bright, close light
  • Keep soil warm for germination, cool for growing
  • Water from the bottom
  • Give seedlings space to grow
  • Don’t rush them—slow and steady seedlings transplant best

With these habits in place, indoor seed starting becomes predictable, successful, and enjoyable.

Seed Starting & Propagation Learning Hub

Start here — Seed Starting Basics: A Complete Beginner-to-Advanced Guide for Indoor and Outdoor Seed Starting

Seed Starting Fundamentals

Planning & Timing

Seed Starting Tools, Supplies & Setup

 Seedling Care, Troubleshooting & Success Tips

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. Harvesttotable.com has more than 10 million visitors each year.

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