What Is A Seed Tray? (Plus How To Water Seed Trays)

Starting your own plants from seed will often give you healthier plants at a lower cost.  If you want to start seeds in bulk, you may want to consider a seed tray to help with germination.

So, what is a seed tray?  A seed tray is a container used to sow multiple seeds at once.  After seed germination, seedlings grow in the seed tray until they are large enough for transplant.  A single seed tray can hold anywhere from 6 seeds to over 1000 seeds!

Of course, when choosing a seed tray, there are lots of options for the material, the type of tray, and the number of cells.

In this article, we’ll talk about seed trays and the options that are available.  We’ll also get into how to use seed trays and how to water the seeds and seedlings.

Let’s get going.

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What Is A Seed Tray?

A seed tray is a container that is used to plant multiple seeds at once.  A seed tray is sometimes called a seed starting tray.

seed tray
A seed tray makes it easier to water and transport seeds and seedlings.

 A seed tray allows you to plant many seeds together in one container.  This makes it much easier to water them and transport them.

After the seeds germinate, the seed tray holds seedlings as they grow, until they are ready for transplant outdoors or into larger containers.

Parts Of A Seed Tray

There are two basic parts to a seed tray, one of which is optional:

  • Tray – this is the outer part that holds soil, individual containers (pots), or a cell flat.  When used with a cell flat, the tray is used for watering from below.
  • Cell flat (plug flat) – this is the optional inner part.  You can put a cell flat inside of a tray to separate seeds from one another. You can get cell flats in various sizes from Johnny’s Selected Seeds.
seedlings in seed tray
A seed tray with a cell flat has a small separate compartment (cell) for each seed.

There are a few different types of seed trays, including:

  • Mesh seed tray – a mesh seed tray allows water to drain out easily.  A mesh seed tray is best for holding multiple individual containers (pots).  A drawback is that the holes in a mesh seed tray are too large to hold soil without it falling through or washing away when watered.
  • Solid seed tray with drainage holes – a solid seed tray with drainage holes allows for adequate drainage, but allows soil to stay moist enough for seed germination.  A solid seed tray with drainage holes is best for planting multiple seeds together in one place.  A drawback is that the seedlings do not have individual cells, so their roots can get tangled together as they grow.
  • Solid seed tray without drainage holes (leak proof seed tray) – a solid seed tray without drainage holes does not allow for any drainage.  A solid seed tray without drainage holes is best for holding a cell flat (also called a plug flat).  Since it holds water, it can be used to catch excess water from watering seeds, or it can be used to water from below (more detail on this later).

You can find all types of seed trays from True Leaf Market.

A cell flat (or plug flat) is a container that is divided into multiple cells.  Some common cell counts for seed trays are:

  • 6 cell seed tray
  • 12 cell seed tray
  • 15 cell seed tray
  • 24 cell seed tray
  • 32 cell seed tray
  • 40 cell seed tray
  • 50 cell seed tray
  • 72 cell seed tray
  • 200 cell seed tray
seed trays
Some seed trays have space for hundreds of seeds in individual cells.

Another interesting option is this seed flat with 20 rows from Johnny’s Selected Seeds. Instead of separate cells, there are separate rows to keep different plant varieties from getting mixed up.

If you decide to use a cell flat for seed germination, each cell should have its own drainage hole.  The tray below the cell flat should be solid without holes if you want to water the seeds from below.

What Can I Use As A Seed Tray?

You can use a wide variety of containers to make a seed tray.  Any container that is leak proof can serve as a seed tray or as cells, including:

aluminum trays
Aluminum trays, often used for catering and food preparation, also make good seed trays.

How Deep Is A Seed Tray?

A standard size seed tray is 2 to 2.5 inches deep.  You probably won’t need cells any deeper than 3 inches.

seedlings in seed tray
Most seed trays have a depth of 2 to 3 inches. Once the roots go deeper than that, it will be time to repot or transplant the seedlings.

The reason is that the length and width of a cell limits the growth of the seedling.  Its roots can reach downward, but they will also spread outwards.

The roots will often hit the sides of the cell before they hit the bottom.  At that point, it is close to the time when you need to transplant the seedlings outdoors or into a larger container.

The size of the cells in a cell flat will vary.  For example, a standard size 1020 tray with 32 cells (4 cells long by 8 cells wide) has cells that are 2 inches long by 2 inches wide.

I know what you’re thinking: 4 cells x 2 inches = 8 inches, and 8 cells x 2 inches = 16 inches.  The extra 2 inches on the length and 4 inches on the width accounts for the space between the cells (the cell borders).

You can learn more about standard size seed trays (1020 seed trays) in my article here.

How Many Seeds Do You Put In A Seed Tray?

The number of seeds you can put in a seed tray depends on a few things:

  • Seed type – the type of seed you plant affects the spacing, and it can vary quite a bit!  For example, if planting microgreens, you can plant the seeds very close together (1/8 to ¼ inch apart) in a tray without a cell flat inside.  On the other hand, tomato seeds might be 2.5 inches apart to give seedlings enough space to grow without getting their roots tangled together. Pelleted seeds are also larger than ordinary seeds.
  • Tray size – the larger the tray, the more seeds you can fit inside.  If you go without a cell flat, you can plant seeds closer together, but you run the risk of the roots getting tangled.  This increases the chances of transplant shock later on.
  • Cell size – smaller cells in a cell flat means more cells in a tray.  However, smaller cells leave less space for seedlings to grow, so you will need to transplant them sooner.
  • Germination rate – if your seeds are old, the germination rate may be low.  In that case, you may want to put more than one seed in each cell, or put seeds close together in a tray (more on this later).
seed tray
The number of seeds in a tray depends on the seed type, tray size, cell size, and germination rate.

How Many Seeds Do You Put In Each Cell?

Usually, you plant one seed per cell in a cell flat.  This gives each new seedling its own space to grow, and you won’t have to worry about plants getting their roots tangled together.

seedlings in seed tray
You may want to plant more than 1 seed in each cell to counter a low germination rate.

However, if the seed germination rate is low, you might not get enough seedlings if you only plant 1 seed per cell.  In that case, you can plant 2 seeds per cell to be safe.

As an example, let’s say the seed germination rate is 90%.  If you plant one seed per cell in a 100 cell tray, you are likely to only get 90 seedlings (90% of 100 is 90).

However, let’s assume you plant 2 seeds per cell.  In that case, the chance of neither seed germinating in a given cell is 1%.  So you would get at least one seedling in 99 out of 100 cells.

The only drawback of planting multiple seeds per cell is that you will have to thin the seedlings later.  You can learn more about how to thin seedlings in my article here.

Do Seed Trays Need Drainage Holes?

As mentioned earlier, it depends what how you are using the tray.

If you are planting seeds directly in the seed tray, without a cell flat, then the seed tray should have drainage holes.  Otherwise, the soil will stay too wet and the seedlings may suffer from damping off.

damping off seedling
If soil stays too wet, seedlings
may suffer from damping off.
Image courtesy of:

If you use the seed tray to hold smaller containers (pots) or a cell flat, then you will need a seed tray without drainage holes.  That way, it can catch extra water after you water your seeds.  You can also use a seed tray without drainage holes to water from below.

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How Do You Water A Seed Tray?

There are two good ways to water a seed tray:

  • Water from below
  • Water from above (use a spray bottle!)

Let’s take a closer look at how each method works.

Watering A Seed Tray From Below

Here are the steps for watering a seed tray from below:

  • First, find a container that is large enough to hold the seed tray.
  • Next, put the seed tray inside the container.
  • Then, add some water to the container (not to the seed tray!).
  • Now, wait until the soil in the seed tray soaks up water from below (through the drainage holes in the tray or the cells).
  • If the soil is still too dry, you can add more water to the container.
  • Repeat this process until the soil is moist enough, and then get rid of the excess water in the container.
plastic container
To water a seed tray from below, find a container that is large enough to hold the tray and and water to the larger container.

This method helps to avoid over watering, and it doesn’t take much time to do it.  However, you do need a large container, and you need to dump out excess water every so often.

Watering A Seed Tray From Above (Spray Bottle)

This watering method is much more straightforward.  All you need is a spray bottle (plant mister) with water in it.

spray bottle head
A spray bottle makes it easy to keep the soil moist when germinating seeds in a seed tray.

Just spray the top of the soil until it gets moist enough for the seedlings.  You may need to do this more often, and it might take a little more time than watering from below.

However, you won’t need to worry about getting a larger container to hold the seed tray or emptying out excess water.

What To Avoid When Watering A Seed Tray

Either of the two methods above will work fine for watering a seed tray.  However, there is one thing you should avoid: do not pour water on top of the soil in a seed tray!

If you do, the water will wash away soil, leaving seeds planted too shallow to germinate properly.  Pouring water on the soil may also wash away the seeds themselves, which will ruin your careful spacing of the seeds.

How Often Do You Water A Seed Tray?

Water a seed tray as often as needed to keep the soil moist.  When soil dries out, even briefly, it can slow down germination or ruin the seeds.

How often you water a seed tray will depend on the humidity, light, and air circulation that the seed tray receives.

seedlings in seed tray
A seed tray in a dry, bright location with good air circulation will need frequent watering.

In a very humid room, water will not evaporate as quickly as in a dry room.  You will need to water more often in a dry house with the heat or AC on high.

If you put your seed tray on a bright windowsill, the sunlight will cause a lot of water to evaporate, and you will need to water more often.  If the seed tray is under a grow light that does not give off much heat (such as an LED), you won’t need to water quite as often.

If your seed tray gets air circulation from a fan or from a breeze on a windowsill, then the water in the soil will evaporate faster and you will need to water more often.

Where To Put A Seed Tray

When deciding where to place a seed tray, heat is more important than light.  The reason is that most seeds do not need light to germinate.

You can find out which seeds need light to germinate in my article here.

After planting seeds, put the seed tray anywhere that is warm enough for the seeds to germinate. You can learn about ways to keep seeds warm for germination in my article here.

The ideal soil temperature for seed germination varies by plant type, but 75 degrees Fahrenheit (24 degrees Celsius) is a good temperature for most plants.

You can learn more about the ideal temperature for seed germination in this resource from the University of California.

Here are a few places you can put seed trays while the seeds are germinating:

  • Windowsill – make sure it gets plenty of sun.  A humidity dome will act as a mini greenhouse and heat up the soil.  Just make sure to avoid drafty windows that could blast sprouted seeds with cold air.
  • Refrigerator – a refrigerator keeps the food cold on the inside, but it does this by releasing heat on the outside.  Specifically, the top of a refrigerator often gets warm due to the heat released.  You can put a seed tray
  • Heat Mat – a seed tray on a heat mat will warm up the soil inside the tray.  This is useful for heating up the soil if you keep your house on the cool side (for example, in the low 60’s Fahrenheit).
  • Under a Grow Light – some grow lights will give off heat (LEDs don’t give off much).  Putting a seed tray under a grow light may heat up the soil if your grow room or house is a little colder than the ideal germination temperature.
sunny window
You can put a seed tray near a bright window, as long as the window is not drafty.

Once the seeds germinate, they will need light – this is true for every type of plant.  If growing indoors, move the seedlings to a place where they can get light from a window or grow lights.

How Long Can Seedlings Stay In Trays?

The answer depends on whether you are using a tray with a seed flat (cells) or not.

Seed Tray With Seed Flat (Cells)

The larger the cells, the longer seedlings can stay in a tray before they become root bound.  If you want to transplant directly from seed trays into the garden, then you will need larger cells.

Some seedlings, such as onions, are transplanted into the garden when they are still fairly small.  In that case, you can probably leave seedlings in the tray until you transplant into the garden.

seedlings in seed tray
Seedlings can stay in larger cells for a longer time before they outgrow the cell (become rootbound).

Other seedlings, such as tomatoes, are transplanted when they are fairly large.  In that case, you might want to repot the seedlings into larger individual containers, perhaps when they are 2 to 4 inches tall.

Then, let them grow a while longer in the larger container.  When they are 6 to 10 inches tall, transplant them into the garden.

You can learn more about when to repot tomato seedlings in my article here.

Seed Tray Without Seed Flat (No Cells)

If you use a seed tray without a cell flat, you will need to watch the seedlings carefully.  If you leave them in the tray too long, their roots will get tangled up.

Plant Roots
When seedlings are grown in a seed tray without cells, their roots become tangled.

This will make it difficult to separate plants when you try to transplant them.  It will also increase the risk of transplant shock, since the roots are more likely to get damaged.

What Can I Use Instead Of A Seed Tray? (Seed Tray Alternatives)

If you don’t want to buy a seed tray, you can recycle materials that you might already have in the house.  For example:

  • Food container – food containers are made of food safe plastic.  You can put soil in the bottom part of the container and plant seeds in it.  Some food containers have separate compartments, which you can use as “cells” for different types of seeds.  If the container has a clear lid, you can use it as a “humidity dome” to keep the soil warmer for seed germination.
  • Egg carton – this is a great option for a biodegradable seed tray.  Put some soil in each “cell” (where one egg was) and plant 1 or 2 seeds in each cell.  When the seedlings are ready for transplant, you can cut or break apart the cells and plant them individually.  The egg carton itself will decompose, so you can leave it in the garden or put it in your compost pile – no waste!
  • Cardboard rolls – this is another great option for a biodegradable seed tray.  Cut a cardboard roll (from toilet paper or paper towels) into shorter lengths (these are the “cells”).  Then, put a bunch of these cardboard “cells” in any tray you have available – it could be a round, square, or rectangular container made of plastic, metal, or wood.  Then, put soil in the cardboard cells and plant seeds in each one.
  • Muffin or cupcake tin – this is an option if you want a reusable seed tray for larger plants.  Put some soil in each “cell” (cupcake or muffin hole) and plant 1 or 2 seeds in each cell.  These cells are probably large enough that you can leave seedlings in them until it is time to transplant outside.
egg carton cardboard
Fill each cell in an egg carton with soil and plant a seed in each cell.

You can learn more about how to make homemade pots for starting seeds in this article from Preparedness Mama.


Now you know all about seed trays and how to water them.  You also know about the different materials and sizes, and how to make your own seed trays.

You can find seed trays from True Leaf Market here.

You can learn about seed starting mix (and how to make it) here.

You can find a full seed starting guide here.

You can learn about more ideas for making your own seed trays in my article here.

You can find answers to some common questions about seed trays here.

You might also enjoy my article on how to promote root growth in plants and my article on using root trainers.

You can learn more about how to water a garden (including when to do it) here.

You can also try using soil blocks as an alternative to seed trays – you can learn more here.

You can learn more about bottom watering plants (and why to do it) here.

I hope you found this article helpful.  If so, please share it with someone who can use the information.

To find books, courses, seeds, gardening supplies, and more, check out The Shop at Greenupside!

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Jon M

Hi, I'm Jon. Let's solve your gardening problems, spend more time growing, and get the best harvest every year!

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