How to Care for Seedlings & Prevent Issues

By Harris Seeds Guest Growing Partner, Tom Stokes Harlow

Starting seeds is one of the pure joys of our work as growers. There’s nothing quite like the thrill of seeing those first green shoots pushing up through the soil. But as you’ve probably already noticed, seedlings can also be heartbreakers. They’re delicate, easily stressed, and vulnerable to a range of problems—chief among them being damping off, that dreaded disease that can wipe out trays overnight.

I’ve lost my fair share of seedlings over the years, and I don’t want you to go through the same steep learning curve I did. So, in this article, I’m going to walk you through not just the basics of seedling care, but also the ins and outs of damping off: what causes it, how to spot it, and most importantly, how to prevent it. Along the way, we’ll talk about treatments, cultural practices, and even chemical options—because as a grower, you always need a toolbox with more than one tool.

Seedling Basics: Building a Strong Foundation

Before we get into damping off, let’s make sure we have the basics of seedling care down. A healthy, vigorous seedling is naturally more resilient to stress and disease, so your best defense starts with strong cultural practices.

Soil Moisture and Watering

The goal is even moisture. Not too wet, not too dry. Seed starting mixes are designed to drain quickly, so water often enough to keep the soil damp but never waterlogged. Allowing the soil surface to dry slightly between waterings will encourage strong root systems. Here’s why: If the soil is always wet at the surface, the small roots your seedlings establish there will not grow, because they are constantly getting their needs met. If the soil is allowed to dry out at the surface, the roots of your seedlings will be forced to grow down, stretching to search for water deeper into the soil. It’s a bit like tough love, but it’s also simply working with the way evolution made them.

If you ever see green algae creeping across the soil surface, that’s a red flag that you’re overwatering. Pull back a little, improve airflow, and make sure your trays have proper drainage.

Hand holding a green spray bottle, misting young green seedlings in black seed trays by a window. Bright, nurturing atmosphere in a home garden setting.

Nutrition for Young Plants

Most seed starting mixes are pretty lean on nutrients. That’s by design—they’re meant to provide a safe, sterile place for seeds to germinate. The more organic matter present in the soil, the more opportunity for creating a habitat for pathogens. However, once your seedlings put on true leaves, they’ll need a boost.

At that stage, start feeding your seedlings with a low-strength, gentle, water-soluble fertilizer once a week, like Neptune's Harvest Tomato & Vegetable 2-4-2. This gives them just enough nutrients to keep them growing strong without the risk of giving their tender roots a chemical burn. Remember: they are tiny – they don’t need much.

Young green seedlings sprout from small soil pods in a tray against a bright background, conveying growth and renewal.

Light and Heat

Thin, stretched, floppy seedlings are usually a sign of poor lighting. Keep your lights directly above the seedlings and close enough that the young plants stay compact and sturdy. If you’re growing in a greenhouse, supplemental lighting on dark days is worth the investment.

Warm soil temperatures are equally important, especially for germination. Seedling heat mats can make a huge difference in keeping roots happy and growth steady. When simulating a seedling’s native environment, soil temperature matters.

Transplanting at the Right Time

One of the most common mistakes I see new growers make is leaving seedlings in their trays too long. A seedling that has outgrown its cell will become root-bound, stressed, and slow to bounce back after transplanting. Seedlings that become overly root-bound might not ever grow. Sadly, they will choke their own roots from being tangled and stuck in a compacted environment.

Check the bottoms of your trays regularly. If you see white roots poking through, it’s time to pot them up or move them into the field. Healthy, unstressed seedlings make for smoother transitions and better yields down the road. Click here to read our transplanting blog.

Damping Off: The Silent Seedling Killer

A small plant with both wilted and fresh green leaves stands on a concrete ledge, surrounded by loose soil. The background is blurred, creating an isolated look.

Now let’s talk about the disease that probably brought you here: damping off.

What It Is

“Damping off” of seedlings is caused by soil-borne fungi and molds—commonly Pythium spp., Rhizoctonia spp., or Fusarium spp. These pathogens thrive in cool, wet, poorly drained conditions with limited air flow. They’re opportunistic, meaning they won’t usually bother a strong, established plant—but seedlings? They’re easy prey.

Damping Off Symptoms

You’ll usually notice damping off in two ways:

Pre-emergence damping off – The seeds germinate, but the seedlings never make it above the soil.

Post-emergence damping off – The seedlings emerge but collapse shortly after. Stems look pinched, mushy, or water-soaked, often right at the soil line. Leaves wilt and turn gray or brown. Roots are often stunted, discolored, or missing altogether.

You might also see fuzzy white mold on the soil surface. Sometimes it takes out whole trays, other times just patches—but either way, it can be devastating.

And here’s the tough truth: Can damping off be reversed? Unfortunately, no. Once a seedling shows classic damping off symptoms, it’s already too late. The key is prevention.

How to Prevent Damping Off

Prevention is 95% of the battle. Here’s what I recommend as a standard practice for every new grower:

Sanitize everything. Used trays, pots, and tools should be scrubbed and disinfected with a 10% bleach solution before reuse. If this sounds daunting, consider Jiffy products for a one-time use, eco-friendly option. Pathogens linger, and a “dirty” tray can undo all your careful work.

Use fresh, clean soil media. Never reuse old potting soil or garden soil for seed starting. Invest in high-quality, sterile seed-starting mix.

Water wisely. Keep things moist but not soggy. Good drainage is your friend.

Maintain warm soil temps. Cold, wet soil is an open invitation for fungi. Use heat mats if needed.

Provide airflow. Gentle air circulation reduces humidity, dries the soil surface, and makes life harder for pathogens. (It’s also like strength training for your seedlings – make them build up “plant muscle” by working to stay upright in a breeze.) Any common household fan will do for home-growers and small batches, or check out our friends at Ken-Bar for ventilation and air flow solutions for bigger greenhouse operations.

Don’t overcrowd. Over-seeding or letting seedlings stay too close together reduces airflow and increases stress.

Young green seedlings sprouting in dark soil-filled plastic trays, arranged in a grid pattern, conveying growth and new beginnings.

These cultural practices go a long way in keeping damping off at bay. Remember, essentially what you are doing is creating a simulation of the ideal outdoor native environment for your seedlings, using supplementary light, heat, soil, and air flow in a controlled way.

Damping Off Treatment Options

A farmer in a checked shirt and vest carefully examines a tray of young seedlings in a greenhouse, conveying focus and nurturing in a farming environment.

Let’s say you’ve spotted an outbreak starting. What then?

First, act fast. Remove and discard any infected seedlings immediately. Don’t try to nurse them back—remember, damping off cannot be reversed. Get them out before they spread pathogens to healthy neighbors.

Second, adjust your conditions. Pull back on watering, improve airflow, and check soil temperatures. Often, small environmental corrections can slow the spread. Harris Seeds always prints the ideal growing specs on their seed packs, so hold on to those after sowing to reference later.

Damping-Off Chemical Control

Sometimes environmental control isn’t enough, especially in larger operations where a loss can mean thousands of dollars. This is where damping-off chemical control can come in.

There are several fungicides labeled for seedling diseases. Products containing mefenoxam, metalaxyl, or fludioxonil are often considered the best fungicides for damping off. That said, always check your crop, label, and local regulations before applying anything. I personally use Tenet Organic Biofungicide.

In my experience, fungicides are most effective when used preventatively (as a seed or soil drench at planting) rather than as a cure after symptoms appear. Think of them as insurance, not a magic fix.

Can Biologicals Help?

Yes! Beneficial microbes like Trichoderma or Bacillus subtilis products can suppress damping-off pathogens and encourage stronger root growth. They’re not a silver bullet, but when paired with good cultural practices, they provide another layer of protection. Just like us, plants benefit from probiotics. You can explore the Harris Seeds options here. Remember – always follow the instructions.

Long-Term Strategy: Building Your System

Seedling production is all about systems. Once you’ve put routines in place for sanitation, watering, fertilizing, and monitoring, preventing problems like damping off becomes second nature.

Here’s my advice to you:

Start every season with a clean slate—sterile trays, clean benches, fresh mix.

Keep records. If you see damping off symptoms, write down when, where, and under what conditions. Patterns will help you fine-tune your prevention plan.

Build redundancy into your system. Extra trays mean you won’t lose an entire crop if one goes bad.

Stay curious. Walk your seedlings daily, observe closely, and trust your instincts.

A person in a brown jacket writes in a notebook with a pen while standing in a greenhouse filled with rows of small potted seedlings, conveying a sense of meticulous care.

The Emotional Side

I’ll be honest: losing seedlings to damping off stings. I’ve been there, staring at a tray of collapsed little stems that represented hours of work and weeks of planning. It feels personal.

But here’s what I want you to remember: every grower has lost seedlings to damping off at some point. It doesn’t mean you’ve failed. It just means you’ve joined the long line of growers who learned the hard way—and who now pass that knowledge forward.

With time, you’ll come to see these setbacks less as disasters and more as lessons. And once you dial in your system, you’ll find damping off becomes less and less of a problem.

Final Thoughts

Strong starts make for strong crops, and preventing damping off is a cornerstone of that. Focus on clean materials, good airflow, careful watering, and warm soil. Use fungicides or biologicals if needed, but lean on prevention first.

Remember, seedlings are vulnerable, but they’re also resilient when given the right conditions. They grow in the wild without our help all the time. With your care and attention, they’ll not only survive but thrive—growing into the strong, market-ready plants your customers are counting on.

And if you ever feel discouraged, just know this: every tray of seedlings you start is a chance to learn, improve, and grow right alongside them.

Here’s to fewer mushy stems, stronger starts, and the satisfaction of watching healthy, vigorous seedlings grow into thriving crops.

Two people outdoors, smiling and tending to seedlings on a table. One sprays water, the other watches. Bright and sunny, with lush greenery around.

Damping Off at a Glance

What It Is	Damping off of seedlings is caused by soil-borne fungi/molds (Pythium, Rhizoctonia, Fusarium) thriving in cool, wet conditions.
Damping off symptoms	Seedlings fail to emerge, or stems collapse at soil line; stems appear mushy, water-soaked; roots stunted or discolored; fuzzy mold on soil.
Can damping off be reversed?	Sadly, no. Once a seedling shows symptoms, it’s too late. Remove and discard affected plants immediately.
How to prevent damping off	- Sterilize trays/tools before use - Use fresh seed-starting mix - Water lightly, avoid soggy soil - Provide good airflow - Keep soil warm with heat mats - Avoid overcrowding
Damping off treatment	Remove infected seedlings, adjust conditions (water, airflow, warmth). Use biologicals (like Tenet Biofungicide Organic) for prevention.
Damping-off chemical control	Preventative seed/soil drenches with fungicides (check crop/label). The best fungicide for damping off often includes mefenoxam, metalaxyl, or fludioxonil.