How to Bottom Water Seed Starts in 5 Easy Steps

Bottom Watered Seeds in Garden


Bottom watering your seedling trays is a wonderful thing, and yet many people struggle with it! But there’s a way to make it work every single time, and it’s a specific combination of the right trays, the right growing medium, and the right watering regimen.

With just a few simple tips, you can get from seeds to healthy seedlings reliably and easily. It does take a little attention to finer details. But once you have it down, it’s easily repeatable, and you’ll be able to grow all those seeds you have waiting to be planted!

Step 1: Start With The Right Tools

Seed starting tray being held by gardener in hands. The seed cell tray has black plastic at the bottom.
Starting with the right tools is essential.

What does a seed need to germinate? For most seeds, that’s warmth and moisture. In a few cases, it also requires light, but that’s less common. Moisture is necessary to penetrate the seed coat and stimulate the embryonic plant to burst forth. Warmth is another way to help indicate to that dormant embryonic plant that it’s time to grow.

Having the right tools at hand to provide both warmth and moisture is crucial. There are many different methods to start seeds. But they all rely on those two factors because no seed will germinate without them.

Growing Medium

Seed starting mix in seed cell trays. Seeds lay on top of the seed starting medium prior to growing.
Starting with the wrong seed starting mix will inhibit germination.

To provide moisture, the best choice is to use a growing medium that’s intended for seed starting. In most cases, a seed starting medium utilizes either peat moss or coconut coir, as both can wick moisture up and hold onto it.

A little bit of worm castings can also help. They can hold up to 10 times their weight in moisture. But you need to ensure that your seed starting mix is fine in particulate size and that it isn’t clay-like or muddy. If you can’t find the right type of mix, there are DIY options that you can use.

Most seed-starting mixes are fine by design; that smaller particle size reduces the chance of air pockets in your growing medium, which means it’s far more likely that the seed will be surrounded by moisture at all times.

In most cases, when we plant a seed, it’s not all that deep (usually not more than 2x the width of the seed itself. In some cases it doesn’t need to be buried at all). But we need that soil to keep moisture against the seed coating for it to penetrate.

Ensuring it’s not clay-like or muddy also makes certain that very young roots can penetrate the soil easily. This will enable the plant to grow.


Soil Temprature Being Measured by a Thermometer. In the background is moist soil that is dark and rich.
You’ll want to ensure that your temperature is warm enough to promote germination.

But what of the warmth? The vast majority of seeds planted in residential gardens will start germinating at about 60 degrees Fahrenheit (15.55 Celsius). Some that are more optimized for warmer temperatures, such as tomatoes meant to grow through the summer months, prefer it a little warmer – say about 70 degrees Fahrenheit (21.11 Celsius). 

You can provide warmth by keeping your plants indoors. Most modern homes are kept in the perfect temperature range for good germination (because we humans seem to like it around 70 degrees!).

But if you can’t start your plants inside your warm and comfy house, there are alternative ways to do it. A greenhouse or hothouse setting works extremely well. So does a seedling heating mat, a device that’s designed to provide optimal warmth for your seed trays.

Seed Cell Trays

Seed Cell Tray that Promotes Bottom Watering. Gardener is holding it with both hands and putting a finger through the bottom where there is holes in the tray.
Using the right seed trays will vastly improve your chances at successful germination.

Finally, you’ll need something that holds the growing medium. I’m a huge fan of our Epic 6-Cell Trays. They have been designed with multiple entry points along the sides and base for water – but there are other options out there, too. 

You’ll also want a tray that can sit underneath; if you’re only starting a few plants, we have germination domes and under trays usable with all of our cell trays, but you can also use a larger tray like our Universal Bottom Tray. Make sure that the bottom tray does not have holes – it has to hold water!

So to recap here, you’ll need the following:

  • Seed-starting medium (nothing with large chunks of wood, rocks, big perlite, or debris in it – it must be fine-particulate and must be able to absorb and hold water)
  • A warm place (indoors, in a greenhouse, or by using a seedling heat mat)
  • Some form of cell trays to hold that growing medium, plus an undertray that can hold water.

Step 2: Get Things Planted

Seedlings planted in epic gardening seed trays. Some are red and some are black with seed starting soil and plants that are labeled in each tray.
Ensure you follow proper seed planting protocol.

Let’s talk about how you want to plant those seeds – because there’s a process here, too.

As I said earlier, most seed-starting mediums are made of peat moss or coconut coir. But there’s a downside: these mediums can become hydrophobic when totally dry.

When a seed starting medium goes hydrophobic, it repels water. That’s what happens to many new gardeners who miss a few too many waterings. The surface turns hard as the material dries out, and the water can’t easily permeate.

To avoid that, you need to start by hydrating your growing medium fully before you plant. Then, you’ll want to keep it moist. 


Gardener using a green plastic bottle to water seed starting mix in a plastic container.
Hydrating your seed starting mix before placing it into trays is important.

Hydrating most seed-starting mediums is easy but takes a little while to do. I personally like to use warm to hot water to do this process. Start by putting your seed starting mix in a large container. You can use an old concrete mixing tray or a large bucket. Add warm to hot water, stir it, and then walk away for about ten minutes.

During that ten minutes, the heat of the water softens the exterior fiber, allowing it to absorb the moisture. By the time you come back after that short wait, there shouldn’t be any water left.

But you’re not done yet. Add more hot water, mix it again, and walk away for another ten to fifteen minutes. If you don’t see any moisture in your container when you come back that time, repeat this process.

Continue to do this until you return and find moisture in the tray. Now it’s fully hydrated; if you grab a handful, you should be able to squeeze water out of it, and that’s good! Your soil should be lightly warm to the touch but not scorching hot, and it will be nicely damp, too.

Filling Your Seed Trays

Gardener holding seed trays with plants inside them in his hand with labels on each of the seed trays.
After moistening the seed starting mix, it’s time to fill up your trays.

It’s now time to fill your seed starting trays with the growing medium. You will find it should be easy to put in there if a little messier than working with the dry stuff.

Once you’ve filled the trays, give the surface of each cell a light press. You aren’t packing the stuff in there, but making sure sure you’ve fully filled the tray. Then, top off any remaining space with more seed starting mix.

Now it’s time to plant the seeds. Earlier, I mentioned that most seeds should be planted about twice their width. Check your seed packet to be sure, but that’s a good general rule of thumb that will work for most seeds.

Smaller seeds usually need to be closer to the soil’s surface than larger ones do. Lightly cover your seeds, and use a finger to gently press down to remove any air pockets around the seed. This ensures your seeds are now fully in contact with the seed starting mix.

Step 3: Keep It Moist

Watering seed Trays with green watering can. The seed trays are green with a rich, moist seed starting mix.
Proper hydration is critical for young seedlings.

Here is where the bottom-watering process begins – and it also includes a little top-watering.

Remember how I said coir and peat could become hydrophobic if allowed to dry out completely? You will need to keep them damp to the touch to prevent that hydrophobic tendency. If you touch the tray’s surface with your fingertip and it seems dry, you need to provide moisture to the surface of the dry cell. You likely need to water the rest of the cell, too.

That consistent moisture, paired with the warmth, will tell the seed it’s time to germinate. But you don’t want to accidentally flush small seeds out of their cell tray by overloading them with water, either.

I like to use a narrow-nozzled indoor watering can to apply water to the surface of my cell trays carefully. If you’re really concerned you’re going to overdo it, use a misting bottle a couple of times a day to keep the top moist.

One thing to note here: if you’re using our 4″ deep Epic 4-Cell trays, these often need that extra top-watering, usually a little more than a misting bottle can provide. This is when that narrow-nozzled watering can really is a benefit; the slender nozzle allows you to very carefully pour onto the cell tray without disturbing the soil.

Germination Domes

Gardener holding plastic seed cells that are covered with a germination dome. The plant is on a wooden table and the gardener is holding it.
Using a germination dome will help to slow water evaporation.

A germination dome can help slow water evaporation from your cell trays. This dome only needs to be on until your plants germinate. So, if you’re using our 6-cell trays, we recommend using the 6-cell germination domes with them – that way, each tray will have its own dome.

As different types of seeds germinate at different rates, you can pop off the domes for each cell tray once the plants have popped up and gained about an inch of height.

Beyond keeping the surface damp, you must keep the rest of the cell damp. And here is where bottom watering comes into play!

Bottom Watering

YouTube video
Watch bottom watering in action by moving to 10:24 in the video above.

In bottom watering, you apply a small amount of water up the bottom and sides of the cell tray. Let the fine medium inside wick the moisture up into the cell tray.

In most cases, it’ll take less than an inch of water to do this. But if you have a lot of cells in the bottom tray, you might want to use up to an inch. This water should be room temperature, not hot. You’re keeping the cells hydrated but aren’t rehydrating them, and you don’t want to damage your seeds.

Bottom watering is a limited-time thing. You do not want your cells to constantly be sitting in a pool of water. Too much bottom watering can be negative and cause soggy conditions that many fungal pathogens will take advantage of. Situations like damping off are common in overly-wet soils.

Let your cell trays sit in the water for about half an hour, but after that, you should pour off any excess water in the tray. This allows the growing medium to wick up that much-needed moisture, but it won’t get oversaturated.

If somehow the trays did absorb too much, they can let that freely drain out into the emptied bottom tray, ensuring that they have exactly the right amount of moisture needed. By avoiding that continual puddle underneath, you’ll have happy seedlings!

Step 4: Monitoring Your Trays

Seed trays are being monitored by gardener as the plants grow. The plants are labeled for the different types that they are. Green plants shoot up from the growing trays.
It’s important to monitor your seedlings as they grow.

There are two ways to test to see if you need to water: by touch and by weight.

Touch testing is by far the fastest. Simply walk up to your tray, lift the germination dome, and touch the top. Does it feel damp to the touch? Then it’s probably fine.

But touch testing only tells you if the very top is damp. It doesn’t tell you if there’s water throughout the tray. To do that, you’ll need to do a weight test.

A dry tray of soil will weigh much less when picked up than a properly-moistened tray of soil will. You can quickly test the difference by filling one tray with dry seed starting mix, and another one with fully hydrated seed starting mix. The fully-hydrated one is what you’re aiming for in terms of weight.

This is not scientific; you don’t need to measure the exact weight of a fully-hydrated tray for optimal watering. But you will get used to lifting the tray and going, “Hm, this seems a bit light,” or “This feels pretty good, I don’t have to water right now.” And by just monitoring those two things – touch and weight – you’ll be able to ensure you’ve got well-watered trays.

One final thing to note here. You’ll want to keep montioring your seed trays if it’s been raining and your trays were left sitting out. This ensures you can pour off that rainwater as fast as possible after the rain ends.

Try not to leave trays of seedlings sitting in that water for too long. Even bringing them under cover while keeping them outdoors during inclement weather is better than letting them sit in water for extended periods.

Step 5: Post-Germination Watering

Gardener holding plants in black plastic seed cells. The plants are fully grown and ready to be transplanted.
Post-germination watering is important for plants to achieve their maximum growth potential.

Your plants have germinated, and new little seedlings are in the trays. They’ve reached about an inch of height, and you’ve removed your germination domes. Now what?

Until the plants need to be potted up into a larger pot or transplanted into the garden, you need to continue monitoring as you have been with the touch and weight tests. But you also want to do it slightly more often.

As a plant puts out its roots and starts to grow, it will need more and more water. This means you’ll likely water more often. And if you’ve got an entire tray of tomatoes, you may be watering twice a day by the time it’s transplant ready. This is because your thirsty little plants will suck up all that water.

Usually, once your plant has developed its first “true leaves” rather than its seed leaves, aka cotyledons, and has reached a couple of inches in height, you’ll see an increase in watering frequency. At that point, it’s actually very tempting to pour a half-inch of water into the tray and just leave it there. Your seedlings will be drinking it more rapidly.

This is fine for slightly more mature plants of 3” or taller, as they can handle it. But between that 1” and 3” height, it’s still best to err on the side of caution. It’s better to water multiple times a day for a half hour of soaking time than to accidentally drown your plants with too much water! 

Besides, your seedlings are still very young and tender. Before their stems start to thicken up, they’re susceptible to damping off. And as someone who’s lost multiple trays of seedlings to damping off, I can tell you it’s no fun.

Final Checklist

Let’s break this all down into a checklist that you can use to tick off the various stages from seed starting to healthy, happy seedlings:

Use the right growing medium, good-quality cell trays that allow for moisture penetration, and if needed, something to warm the soil to the right temperature. Have germination domes and bottom trays that hold water.

Fully hydrate your seed starting mix before planting, and when you plant your seeds, lightly press to ensure that the fine seed starting mix makes full contact with the seed.

Keep the top surface of the trays damp to a touch test (germination domes can help with this). Lift the trays to confirm that they feel like they still are holding moisture. Keep the germination domes on until your seedling plants are about 1” tall.

Once the germination domes come off, check consistently (at least once a day in cool weather, at least twice a day in warm weather), doing both a touch test and a weight test. If the surface is dry, top water; if the tray feels light, give it about 30 minutes of bottom watering, then pour excess moisture out of the tray.

When your plants get larger, they will need more water. Resist the temptation to leave them sitting in a pool of water – this can create the conditions in which many fungal pathogens thrive. Water more often until it’s time to transplant them into the garden or put them in a larger pot. 

All in all, this is an incredibly easy process. But most new gardeners usually have one or more of these things out of whack. Perhaps they used the wrong soil for seed starting, and it doesn’t wick the moisture well, or they aren’t using a tray which allows for good moisture penetration (or good drainage). Or, they’ve provided an overabundance of water, and the seedlings drowned. 

We have all killed a few seedlings at one time or another, so messing up isn’t the worst thing in the world. But now you’re armed with the knowledge to avoid these errors in the future!

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