Starting your seeds in trays is a smart choice. Done correctly, it provides more timing flexibility, control, and ultimately better germination outcomes vs. sewing direct-in-ground. That said, it’s not without its own challenges and you may find yourself frustrated with wasted seeds failing to germinate. Consider if one of these issues could be the cause.

Note this list is specific to germination, not the seedling phase which brings a separate set of conditions to watch out for!

1. Your Seeds Have Gone Bad

Sometimes a bad germination rate really wasn’t caused by anything you did. Hooray! Unfortunately, seeds do go bad, especially if stored in an opened paper packet.

Think back: did your seed packets go through any huge temperature and humidity fluctuations? Are they years and years old?

If so, your best bet is simply to get some fresh ones. And remember that even fresh, quality seeds will not have a 100% germination rate no matter the conditions.

2. Your Seeds Require Light to Germinate and Aren’t Getting it

Did you know that seeds from certain plants like Chamomile actually require light to germinate? Check if your struggling seeds fall into this category and, if so, try again. Except this time firmly press the seeds into the top of the soil rather than cover them.

Watering needs to be very gentle for seeds planted in this manner to prevent them from being washed away.

3. Your Seeds are Rotting in Waterlogged Soil

Seed cells that are consistently waterlogged are low in oxygen. This environment leads to rotted seeds rather than seedlings.

Beyond the obvious advice of water less, try also watering from the bottom by slowly adding water to a flat tray placed underneath the seed tray.

It’s also a good idea to sanitize the tray and fill it with fresh soil and seeds. It’s very easy for a fungal infection to creep in during the overwatering period and exacerbate the issue.

4. Your Seeds are Compacted in Dense Soil

The environment in a seed tray is missing the beneficial aerators like worms and roots from mature plants that you’d find in an outdoor garden. Which is why it’s important you don’t use unamended native soil from your yard for best germination results. In fact, common DIY potting mixes contain as much as ⅓ peat moss (an ingredient we don’t advocate using) and ⅓ vermiculite to create an extremely loose, oxygen-rich soil environment.

If your soil is too compact, the easiest way to fix it is to replace it with a premade potting soil or seed starter. Alternatively, you can mix it with ingredients like perlite and coco coir.

5. Your Seeds Can’t Germinate Due to Extreme Temperatures

Temperature gets a lot of blame as the culprit behind poor germination. Probably too much blame.

It’s true that extreme temperatures will prevent germination, but for most folks living in a house with a thermostat, it’s not the first thing to consider if your trays are inside. Check out this handy chart to learn the minimum and maximum temperatures some of our favorite plant seeds will germinate at. If you’re surprised at the ranges, you’re not alone! I was too.

If you still suspect temperature to be the cause, your best bet is to introduce a seedling heat mat. They’re good at reducing germination times anyhow, so not a bad purchase even if temperature doesn’t turn out to be the root cause!

6. Your Seeds Require Cold Stratification First

If you’re growing primarily fruits and vegetables, you may not need to worry about cold stratification. But if you’re working on perennial wildflowers, you may actually need to mimic a cold season first. This is most commonly accomplished by putting the seeds onto a moist medium like paper towel, then into a container, then into the fridge. But be sure to check to verify it’s necessary for your seeds before giving this a shot though!

P.S. If you want to go back and get a primer on how to start seeds in trays, we’ve got you covered.