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Microgreens Trays With or Without Holes: Which Setup Works?

by Serge••2
Red amaranth microgreens
Getting Started

Two nearly identical trays can create very different growing days.

A beginner sets one black tray on the counter, adds damp growing mix, sprinkles seed, and feels ready—until water pools in one corner or slips onto the shelf underneath. Another tray may look the same at first glance, but a few small holes change everything once soil, roots, and rinsing are involved.

The real question is not whether microgreens trays must have holes. It is how water moves through the setup. Holes let extra moisture drain away; solid trays hold water where it lands. Either can work, but each asks for a different watering habit, a different bottom tray arrangement, and a little attention to leaks before the crop is sitting beside a windowsill or kitchen counter.

Short answer

Both tray styles can work

  • Holes drain A tray with holes lets extra water escape, which lowers the odds of soggy roots and sour-smelling growing medium.
  • No holes catch A solid tray catches runoff, protects shelves and counters, and makes bottom watering much tidier indoors.
  • Together is easier For many home growers, the easiest setup is a perforated growing tray nested inside a solid catch tray.
  • Solo needs care Single-tray setups can still work, but they need closer attention to water amount and where overflow goes.

A forgiving starter setup is often one tray with drainage holes sitting inside one tray without holes. The top tray holds the soil or mat; the bottom tray catches drips and can hold a shallow layer of water for bottom watering.

This pairing does not remove all guesswork, but it gives extra room for small watering mistakes—especially on kitchen counters, windowsills, or wire shelves.

Moisture control

Why holes make watering easier

Drainage gives roots breathing room and makes small watering mistakes less risky.

Perforated trays are popular because they let extra water leave the growing layer instead of sitting around the roots. That matters most with soil or coco coir, which can hold moisture for a long time after watering. Without drainage, a heavy pour can turn the tray into a shallow swamp, especially near the corners where water tends to collect.

Holes make the setup more forgiving. If the medium is slightly overwatered, the excess can drip into a solid catch tray underneath. This does not remove the need for good watering habits, but it gives beginners a wider margin before problems like sour-smelling soil, algae, or weak, stretched growth show up.

A perforated tray also makes bottom watering microgreens trays simple. Water goes into the solid tray below, then the soil or coco absorbs moisture upward through the holes. The stems and leaves stay drier, the surface is disturbed less, and watering tends to feel more even across the tray.

A practical pairing is one tray with holes nested inside one tray without holes: drainage above, leak protection below.

The trade-off with drainage

Holes help water move, but they also need somewhere to drain.

Perforated trays make watering feel more forgiving because excess water can escape before the root zone stays soggy. That is especially helpful with dense sowings, shallow soil, or growers still learning how much water a crop actually uses.

The catch is practical: holes turn every watering into a runoff-management task. On a kitchen counter, shelf, or windowsill, even a small leak can leave muddy rings, damp towels, or water under grow lights. A tray with holes usually works best when it sits inside a matching solid tray, so drainage is captured instead of becoming a mess.

That paired setup is common in many home microgreens supply setups because it separates two jobs: the top tray holds the growing medium, while the bottom tray catches water and protects the surface underneath.

Solid trays have a real job

They keep indoor growing cleaner and easier to manage.

A solid tray is not simply the “lesser” option. It can be the right tray when spills matter more than perfect drainage, such as on apartment counters, wooden shelves, classroom tables, or anywhere water damage would be annoying.

Solid trays are useful for:

  • Bottom trays, catching runoff from a perforated tray above.
  • No-leak growing, when watering is done carefully and lightly.
  • Soaking or pre-moistening mats, especially with hydroponic pads.
  • Transporting trays, since water and loose soil stay contained.

The main caution is that solid trays leave less room for mistakes. If too much water is added, it has nowhere to go. Many growers handle this by watering in smaller amounts, tipping out visible standing water, and checking the weight of the tray rather than watering on a strict schedule.

For tidy indoor growing, solid trays are often part of the system rather than a compromise. A perforated tray may manage the root zone, while a solid tray keeps the room clean. Together, they make microgreens easier to grow in real living spaces, not just in ideal grow-room conditions.

The main risk with a no-hole tray

Solid trays can grow microgreens, but water management becomes less forgiving.

Planting directly into a solid tray is not automatically a problem. Many small indoor grows use this setup successfully, especially with a shallow layer of medium and careful watering. The catch is that extra water has nowhere to leave the tray, so mistakes tend to sit at the bottom.

When the lower part of the medium stays wet for too long, the surface can still look normal while the root zone is becoming soggy. That trapped moisture may lead to slow growth, weak stems, or patches that collapse before harvest. In some cases, stale water at the bottom can create a sour or swampy smell.

Low airflow makes this easier to notice. A dense canopy, a warm room, or trays packed closely together can keep humidity high around the crop. With no drainage holes, the grower has fewer ways to correct an overwatered tray besides waiting, increasing airflow, or gently tipping off excess water if possible.

A solid tray works better when watering is light and even. The medium should feel moist, not muddy, and the tray should not slosh when moved. Small, frequent watering adjustments are usually safer than adding a large amount at once.

Simple check before watering again

Lift one corner of the tray gently. If it feels heavy, smells stale, or the lower medium looks shiny and saturated, waiting a little longer can help prevent the bottom layer from staying waterlogged.

Choosing by method

Match the tray to the way the greens are grown

  1. Soil or coco grows
    Loose media usually benefits from a tray with holes nested inside a solid catch tray. The upper tray can drain after misting or bottom watering, while the lower tray keeps shelves and counters clean.
    Look for
    A perforated growing tray with a snug, solid bottom tray for runoff control.
    Avoid
    Planting deep, wet media in a solid tray with no escape route for extra water.
  2. Grow mats and shallow media
    Hemp, jute, paper, or thin coco mats can work in solid trays because they hold a more predictable amount of moisture. They still need attention, especially around corners where water can pool or dry out unevenly.
    Look for
    A shallow solid tray when the mat is thin and moisture is checked often.
    Avoid
    Letting mats sit in puddles, or assuming a solid tray means less monitoring.
  3. Hydro-style setups
    A no-hole tray can make sense when water is intentionally held below the roots, especially with pads, mesh inserts, or a second support layer. The key difference is that the tray is being managed as a small reservoir, not as a pot full of soaked media.
    Look for
    Clear separation between roots, support material, and standing water.
    Avoid
    Turning a soil tray into a reservoir without airflow around the root zone.
  4. Seeds, humidity, and daily attention
    Dense crops such as broccoli, radish, and mustard can trap moisture quickly, while larger seeds like peas and sunflower often need more structure and airflow. In humid rooms or for growers who check trays less often, holes add a helpful safety margin.
    Look for
    More drainage and airflow for dense sowing, large seeds, humid rooms, or irregular watering checks.
    Avoid
    Pairing heavy seeding, still air, and a sealed wet tray for several days at a time.
Routine

A tidy nested-tray routine

  • Set the perforated tray inside a solid tray.
  • Mist or lightly top-water until seeds root.
  • Switch to bottom watering once roots reach down.
  • Add a shallow amount, then check later.
  • Empty stale standing water; keep trays clean between batches.

Standing water is a holding zone, not storage. A little can hydrate roots; too much can turn sour, especially in warm, still rooms.

Holes or no holes

Donny Greens discusses whether microgreen trays need holes, a useful companion when comparing nested drainage trays with direct planting in solid trays.

Buying check

Durability matters more after the first batch

  1. Stiffness when full
    A tray that feels fine empty can twist once wet medium and dense greens add weight. For repeated crops, sturdier trays for repeat growing are usually easier to lift without flexing or spilling.
    Look for
    A rim and base that stay fairly rigid when lifted with one hand at each end.
    Avoid
    Very floppy trays that bow sharply, especially when nested or moved to a sink.
  2. Usable depth
    Shallow trays dry faster and may leave less room for roots, while deeper trays hold more medium and moisture. The useful middle ground depends on crop height, watering style, and shelf clearance.
    Look for
    Enough depth for an even medium layer without crowding lights or shelves.
    Avoid
    Buying extra-deep trays just for strength if they make watering checks harder.
  3. Cleaning and reuse
    Microgreen trays get scraped, rinsed, and dried often. Smooth corners and plastic that tolerates repeated washing can make reuse less frustrating.
    Look for
    Surfaces that rinse clean without many ridges catching roots and debris.
    Avoid
    Brittle plastic that cracks at corners after a few washes.
  4. Trial versus routine use
    Thin trays can be perfectly reasonable for testing varieties or learning a setup. Once batches become regular, durability often saves annoyance more than it changes the grow itself.
    Look for
    Budget trays for experiments; thicker trays for steady rotation.
    Avoid
    Overbuying premium trays before knowing the preferred growing routine.
Space planning

Fit can matter as much as holes

A tray setup works better when the pieces actually match. Many microgreens growers use a perforated tray inside a solid tray, so nesting compatibility matters: the top tray should sit securely without wobbling, bowing, or leaving a big gap that wastes space.

Standard 10 x 20 trays are popular because they fit common shelves, humidity domes, and grow-light layouts. Smaller trays can be easier to move and rinse, but they may create awkward gaps on a rack. Before buying several packs, it helps to compare tray sizes that fit the growing area, sink, storage shelf, and light footprint.

Good drainage is useful, but a tray that fits neatly is often the difference between a tidy routine and constant rearranging.

FAQ

Quick tray decisions

Should microgreens trays have holes?

Holes are useful when drainage matters or bottom watering is part of the routine. They give excess water somewhere to go, especially with soil or coco mixes.

When does a solid tray make sense?

A no-hole tray helps contain water, soil, and mess on shelves or counters. It can also act as a shallow reservoir when a perforated tray sits inside it.

Is using both trays worth it?

For many indoor setups, a perforated tray nested in a solid tray is the most forgiving option. The top tray drains; the bottom tray catches runoff and allows gentle bottom watering.

What changes the decision?

Crop density, seed size, growing medium, airflow, and watering habits all matter. A careful light-watering routine can work in solid trays, while heavier watering favors drainage.

Conclusion
  • Holes favor drainage and bottom watering.
  • No holes favor containment, reservoirs, and cleaner shelves.
  • A nested pair gives extra margin for small indoor growing spaces.

There is no single tray style that fits every batch. Perforated trays suit growers who want drainage and bottom watering, while solid trays suit tidy containment and reservoir-style watering.

For a simple indoor setup, the paired approach is often the easiest to manage: one tray with holes inside one tray without holes. The better choice still depends on the crop, medium, and how wet the routine tends to run.

Serge has been growing microgreens on his kitchen windowsill and fermenting vegetables for years — driven by the same instinct that runs through everything he does: figure out how a system works, then make it better. SlowLarder is where he documents what actually works, batch by batch.

2 thoughts on “Microgreens Trays With or Without Holes: Which Setup Works?”

  1. I appreciate the balanced take here. A lot of microgreens advice treats holes vs no holes like a moral choice, lol.

    For people growing in apartments, the solid bottom tray is non-negotiable unless you enjoy explaining sunflower runoff to your landlord.

  2. What about tiny seeds like amaranth or basil? I’ve had them dry out on perforated trays because I’m scared of bottom watering too early, but solid trays got funky fast when I covered them for germination.

    Maybe this is more about humidity domes than holes, but I’d love a quick rule of thumb for the really small-seeded stuff.

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