Microgreen Trays With Holes vs. Without Holes: Which Setup Works Best?

The upper tray with holes holds the growing medium and seeds. The solid tray underneath catches drainage and can temporarily hold water for bottom watering. This setup helps manage moisture while containing runoff on indoor shelves, counters, or growing racks. Penn State Extension and University of Maryland Extension

You can grow microgreens in a tray without holes, but it requires closer watering control because excess water has no route to drain away.

Important context: This comparison applies mainly to tray-grown microgreens in loose media, such as coconut coir or seed-starting mix. Growing mats and other systems can use different watering methods.

A tray with drainage holes is typically used as the upper planting tray when microgreens are grown in loose media. The holes allow excess irrigation water to leave the growing medium rather than collecting at the bottom of the planting tray.

Drainage does not make overwatering impossible. Watering volume, frequency, room conditions, and the growing medium still matter. But a perforated tray provides a path for excess water to move into a separate catch tray below.

Penn State Extension recommends containers with drainage holes for microgreens, noting that this arrangement allows excess water to drain and supports bottom watering without directly wetting the greens. Penn State Extension

In a bottom-watering system, the planted tray with holes sits inside or above a solid tray without holes. Water is added to the lower tray, and the growing medium absorbs moisture through the holes in the upper tray.

The University of Maryland Extension describes this type of arrangement as a drainage tray containing medium and seed set inside an undrained tray that acts as a water reservoir. University of Maryland Extension

Bottom watering can limit direct irrigation water on the leaf canopy. That can be helpful for moisture management, but it does not by itself prevent mold, damping-off, or other crop problems.

Bottom watering is common, especially after seedlings are established, but it is not the only workable approach. Some growers use gentle top watering during early growth or when the surface of the medium needs moisture.

If top watering, use a gentle method that does not disturb seeds, compact the medium, or damage young seedlings. University of Illinois Extension describes using a spray bottle or delicate water breaker for microgreen watering. University of Illinois Extension

A solid tray without holes has two practical jobs in a nested system:

This makes solid trays especially useful indoors, where water running off a planted tray can create a mess or damage shelving and surfaces. Utah State University Extension and Virginia Cooperative Extension both describe bottom-watering methods that use a planted perforated tray with a solid tray underneath. Utah State University Extension Virginia Cooperative Extension

The goal is evenly moist growing medium—not medium that remains continually saturated.

After adding water to the lower tray, allow the growing medium to absorb moisture, then assess whether water remains. Utah State’s example bottom-watering method includes discarding water left in the lower tray after the growing medium has had time to absorb what it needs. The appropriate water amount and timing will vary with the crop, medium, tray size, temperature, and stage of growth. Utah State University Extension

University of Maryland Extension similarly advises keeping growing media moist rather than saturated. University of Maryland Extension

A second tray can also serve as a cover during germination in some microgreen workflows. Covering a newly seeded tray may help maintain darkness during an early blackout period, and some methods add gentle weight above the seeds.

This is not required for every crop or method. Whether to use a cover depends on the variety, seed size, growing medium, and your own growing process. Utah State University Extension

For many loose-media home grows, a tray pair makes watering and cleanup easier:

Penn State, the University of Maryland, Utah State, and Virginia Cooperative Extension all describe versions of this basic drainage-and-bottom-watering approach. Penn State Extension University of Maryland Extension Utah State University Extension

This is a practical framework, not a fixed recipe. A dense tray in a warm, dry room may use water differently from a lightly seeded tray in a cooler, more humid space.

A “1020” tray commonly refers to a greenhouse-flat format around 10 by 20 inches. However, the label does not guarantee that every tray has the same exterior dimensions, interior growing area, depth, rim shape, or nesting design.

Before buying a pair, check the product dimensions and confirm that the specific holed tray is intended to fit inside the solid tray you plan to use. This is practical purchasing guidance, particularly if you want to bottom water or stack trays during germination.

Yes. A solid tray without holes can be used as a planting tray.

The limitation is simple: if too much water is added, it remains in the tray unless you carefully pour it off. With no drainage route, it is easier for loose growing media to stay excessively wet.

For growers using loose media, a solid tray can work, but it requires closer observation and more careful watering than a perforated tray placed inside a lower catch tray.

A perforated tray does not eliminate overwatering risk, but it provides a drainage path if too much water is applied. That can make moisture management more forgiving for newer growers.

For that reason, a holed planting tray paired with a solid lower tray is often a practical starting point for indoor loose-media growing.

Drainage holes can help by:

The growing medium needs to retain enough moisture for roots while still allowing adequate aeration. Research on microgreen substrates supports the importance of balancing water-holding capacity and air capacity in the root zone, though it does not establish a best tray-hole pattern. Peer-reviewed substrate research

Drainage holes do not, by themselves:

Moisture-related crop problems depend on more than tray design. University guidance emphasizes the importance of avoiding saturated media, maintaining airflow, using clean equipment, and managing the growing environment. University of Maryland Extension Virginia Cooperative Extension

Tray choice is only one part of a successful microgreen setup. Also pay attention to:

Bottom watering can be useful, but it does not replace sanitation, airflow, or careful observation.

A 1020 tray is a common greenhouse-flat format around 10 by 20 inches. Before buying, confirm:

Because microgreens are eaten, use clean containers suitable for food production. Penn State Extension recommends clean growing materials appropriate for food production, including containers with drainage holes when using a bottom-watering setup. Penn State Extension

Repurposed containers are not automatically unsuitable, but avoid using containers that are heavily worn, difficult to clean, or of unknown intended use.

Tray depth affects how much growing medium a tray can hold, how high the rim sits above the medium, and how the tray handles during watering and harvest. Shallow containers are commonly used for microgreens, but there is no single tray depth that suits every crop and growing method. University of Maryland Extension

Choose a format that fits your medium, shelf space, watering routine, and harvest method.

After harvesting, remove roots, spent growing medium, and visible debris from both trays. Doing this promptly makes the next cleaning step easier.

Reusable trays should be thoroughly washed between crop cycles. Cleaning removes visible soil and residue; sanitizing or disinfecting is a separate step intended to reduce microorganisms on an already cleaned surface.

Follow the directions on the cleaning or sanitizing product label, including any required dilution, contact time, and rinsing instructions. Illinois Extension emphasizes that reusable pots and trays should be thoroughly cleaned before disinfection. University of Illinois Extension

Virginia Cooperative Extension also identifies sanitation as an important part of managing plant and foodborne pathogen risks in microgreen production. Virginia Cooperative Extension

Allow trays to dry and inspect them before the next crop. Replace trays that are cracked, difficult to clean, or no longer work well in your watering setup.

Tray hygiene depends primarily on residue removal, cleaning, sanitizing, drying, and handling—not simply on whether a tray has holes.

https://extension.psu.edu/a-step-by-step-guide-for-growing-microgreens-at-home

https://extension.umd.edu/resource/growing-microgreens-and-baby-greens-indoors

https://extension.usu.edu/yardandgarden/research/grow-your-own-microgreens

https://www.pubs.ext.vt.edu/SPES/spes-756.html

https://extension.illinois.edu/sites/default/files/growing_microgreens_1.pdf

https://extension.illinois.edu/blogs/commercial-fruit-and-vegetable-growers/2024-02-20-southeastern-illinois-olney-update-options

https://www.lsuagcenter.com/articles/page1625257098667

https://pmc.ncbi.nlm.nih.gov/articles/PMC7139710/

https://pmc.ncbi.nlm.nih.gov/articles/PMC10352662/

https://andisway.com/products/growing-trays-with-drain-holes