Caring for your own plant nursery for the very first time is no easy task. There are a lot of things you still need to experience as a first time gardener. Starting seeds indoors and keeping those seedlings alive requires a lot of effort, skill and observation.

I’ve written about seedling mistakes before, and improper watering is by far the most frequent mistake new gardeners make. So I’ve decided to devote an entire article on watering seedlings. We’ll cover watering methods, signs your trays need watering and how often to do it for optimal seedling health.

Indoor seedlings need watering every couple of days, depending on their age, tray size and soil aspect. Check your seedlings daily and only water them when the top soil has completely dried out and the trays feel lighter. You can bottom water or spray water from above – or a combination of the two.

It’s easy to kill your indoor seedlings with love (a.k.a overwatering), but before you pick up your watering can, you need to check the signs and see if your baby plants are truly thirsty. Here’s what to look for:

WHEN to water: signs your indoor seedlings need watering

Your growing environment, as well as your seedlings, will give you clues on when to water if you really know what you’re looking for:

  1. The top 1cm of the soil is dry and turning a lighter color.
    If you check the humidity by sticking your finger inside the container or trays (careful as not to disturb the roots), you’ll notice that the soil mixture is not completely dry all the way down.
    A dry layer of soil on top is a good indicator that it’s time for watering, and it’s also a good way to prevent green mold or algae from forming on top of the surface.
    Always wait for the top soil to dry out in between waterings.
  2. The trays are starting to feel lighter.
    To confirm that the soil mixture is drying out, you can lift the trays and feel their weight.
    Module trays should feel heavier when waterlogged and very light when completely dry. You’ll soon learn the optimum weight through trial and errror.
  3. Young seedlings are starting to look droopy and leaves on older seedlings won’t look as plump.
    Young seedlings suffer the most from water variations, and when they’re starting to go soft and look like they’re wilting, they need water immediately. Try to keep them under observation and not allow them to get to that stage.

HOW OFTEN to water your indoor seedlings

On average, your seedlings will need watering every 48 hours. Water them daily or twice a day, and you risk getting poor germination or disease. So it’s best to err on the underwatering side.

When they’re young, seedlings need more consistency. Young, small seedlings start their life in small module trays which don’t hold on to a lot of water and tend to dry out quickly. That’s the most sensitive part about starting seedlings – finding the right sized tray so that it’s space-efficient while also providing enough water and room for roots to develop.

The smaller the module tray, the harder it is to get watering right. So check your seedling every day, even twice a day at first, and only water when you see the signs described above: dry top soil and light trays. Don’t overwater thinking you’re giving your seedlings extra moisture to last them longer, it doesn’t work that way and too much water will deprive their roots from oxygen.

Now let’s take a look at how to water older seedlings. Seedlings that need to spend longer periods indoors – like peppers and tomatoes – benefit from larger containers. We either start the seeds in larger nursery pots or move them into bigger containers once they’ve grown to a decent size.

Watering rules for larger containers are different – you can water the older seedlings grown in larger containers as little as twice per week. A good rule of thumb is to stick your finger inside the soil. The “finger dip” test is also used with house plants – if the soil is dry up to the first finger knuckle, it’s best to water your seedlings.

5 factors that influence the need for watering

Just like outdoor seedlings have to withstand temperature variations, wind, rain, or drought, so do your indoor seedlings, but on a different level.

The microclimate you’ve created inside your growing room will affect how much water your seedlings will need:

  1. Temperature – most seedlings need higher temperatures to germinate – 68F to 86F (20C to 30C). This means that you’ll either warm up your room or use heating mats underneath your trays. To prevent water from evaporating too fast, stop using heating mats as soon as the seeds have germinated or turn the heat down to below 68F.
  2. Type of grow lights – fluorescent grow lights give out much more heat compared to LED ones. You also need to keep them much closer to the soil surface which can result in quicker evaporation. Keep this in mind when using these types of lights.
  3. Soil mixture – not all seed starting mixes are created equal. Compost is great at retaining moisture but poor with draining. Coco coir and peat moss drain well and will retain water, but once completely dry, it’s difficult to get them rehydrated again.
  4. Tray or container size – small module trays suffer from quick evaporation, while bigger containers don’t need watering as often, but take up more space underneath your lights.
  5. Room ventilation – improper ventilation and overwatering are a fatal combination for seedlings and often lead to damping off and green mold growth.

HOW to best water your indoor seedlings

You can water your seedlings in one of two ways, and each have their purpose:

Top watering or misting

Misting is reserved for starting seeds, when your top soil needs to stay relatively damp. You can mist the surface daily or use a humidity dome – either way is fine. Once you see seedlings popping up, reduce the amount of misting – you may see some uneven germination, so keep misting from above for a couple more days until most seeds have germinated.

If it’s been more than a week and only a few of your seeds have germinated, top misting won’t help anymore. You probably have an issue with old seeds or you’ve overwatered your soil mix for too long, causing seeds to rot.

Bottom watering

This is the preferred method of watering for indoor seedlings. For bottom watering, lift the module tray up, enough for a watering can nozzle to fit, and pour water inside the bottom tray. Fill the trays with about 1/2 inch of water. Wait for 20-30 minutes, check if all the water has gone, and either add some more or pour the excess water out.

You can also check the trays to see if they’re heavier. The top soil will be dry for a while and won’t turn wet right away, but it might do so in a couple of hours, depending on how much water you added.

Seedlings in larger containers will also benefit from bottom watering, but the key thing to mention here is that you don’t need to see your top soil turn wet. Use the finger dip test every day to see if their water levels are ok.

Soil troubleshooting

If you’re using peat moss as your seed starting mix, you may notice some issues when going too long in between waterings. When peat moss completely dries out, it almost looks like it’s water repellant. You pour water from above and it seems to run off the surface. You water it from the bottom and it doesn’t look like anything is happening.

This is when your peat moss mixture needs a good soaking. Fill the trays with double the amount of water you would normally add, and let the module tray filled with peat moss float inside for about 30 minutes. If it doesn’t appear soaked from above, repeat the process and also mist the soil from the top.

It’s hard to find the perfect growing medium, so I like not to exclusively use coco coir or peat moss, but also mix it with some organic matter like vermicompost for added moisture retention and nutrients.

Can seedlings recover from underwatering?

Short answer – YES. If you catch underwatered seedlings in time, before they dry out completely, they will recover from overwatering.

Onion seedlings and generally taller seedlings are an excellent example of this. Whenever they suffer from underwatering, they go limp and start to fall over, but spring back up as soon as they’ve had a good soak.

You might think that yellowing leaves are a sign of underwatering, but it’s quite the opposite. It’s overwatering that causes the most distress, drowns the roots and robs them of oxygen. Yellowing of the cotyledons (first bottom leaves) is perfectly normal though, and it’s just a sign that the plant is getting a little too old or too large for its tray.

Can seedlings recover from overwatering?

If you catch overwatered seedlings in time, you might still be able to fix the problem. However, prolonged overwatering will lead to 3 major problems:

  • Damping off disease – a soil borne pathogen that causes rotting of the stem and affects roots on very young seedlings. It only attacks seedlings in damp and cool conditions. Once the seedlings fall over and rot at the stem, there’s no more saving them. So if you notice this, know that they won’t recover.
  • Root rot – if water is constantly left in the bottom trays, it can lead to root rot. Seedlings affected by root rot will have stunted growth and yellow leaves. Eventually, root rot takes over the entire ball root and the seedling can no longer be saved. At this point, it’s best to start again with fresh, healthy seedlings, rather than focus on saving weak ones.
  • Overwatering will also cause mold to appear. Whether it’s white fuzzy mold, green mold or green algae on top of your seedling soil, it’s no good news for your seedlings. Fortunately, mold itself won’t kill your seedlings, but it’s a good indicator that the growing environment and water levels aren’t ideal.

To help your seedlings recover from overwatering, drain all the trays and wait for the top soil to dry out. You can also install a ventilator or leave the windows open if it’s not too cold outside. It may take a couple of days, but the excess moisture will eventually wick out.


Watering your indoor seedlings is one of those crucial skills that you have to master through trial and error. I’ve lost countless batches of seedlings to damping off disease until I realized what I was doing wrong. But once I got my temperature and ventilation right, as well as learned to read the soil and health of my seedlings, I was off to a great start. With research and patience, you’ll get there too.

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