11 Seed Starting Mistakes to Avoid This Season

Are you seeding your plants indoors under grow lights, or directly into the ground this season? If so, there are many mistakes you can make if you aren't careful. In this article, gardening expert and former organic farmer Logan Hailey shares some of the top mistakes gardeners make when planting their seeds in the spring.

seeding mistakes

Sowing seeds is one of the most exciting parts of gardening. You bury a little seed in the soil with all the hope and faith that it will soon grow into a fruitful tomato plant or abundant squash patch. But if your seeds don’t germinate or they die early on, your whole garden season could be thrown off.

There are a number of common mistakes that gardeners make when starting seeds both indoors, and outdoors. Problems like adequate light and not enough water can be tricky when starting seeds indoors at the end of winter.

Fortunately, planting millions of seeds over the course of 8 years of organic farming taught me some industry secrets! Let’s dig into the most common seed-starting mistakes I’ve seen, as well as how to avoid them so you can start your season off with healthy, growing plants!

Forgetting to Thin

Close-up of female hands thinning microgreens with scissors on a beige table top. Microgreens grow in a square transparent plastic tray. The sprouts have tall, pale green stems and round, dark green leaves.
It is recommended to thin out weak seedlings so that the plants do not compete for space, water and light.

Thinning is essential for any successful garden. You have to cut out the weaklings so the strongest, healthiest seedlings can thrive. If you don’t thin, you may end up with dozens of weak plants that barely yield anything at all.

The plants will be struggling to compete for space, water, nutrients, and sunlight. This is especially true for any vegetable that requires a lot of space to thrive, such as tomatoes, cucumbers, squash, or cauliflower.

You may be thinking, “I paid all that money and spent all that time on those seeds!” This is true, but if you avoid thinning, you will actually lose more yield in the long run. Without adequate spacing, those baby plants will never grow to their full glory.

For example, a bed of carrots sown every ½” will ultimately yield a bunch of tiny, spindly carrots that barely fill your harvest basket. Carrots that are properly thinned to 1-2” between every plant will likely yield plump, crunchy roots that are perfect for fresh-snacking or roasts.

The number of roots doesn’t matter (who wants a billion toothpick carrots?). Thinning is about prioritizing the quality, flavor, and weight of your harvest!

How to Avoid It

Look at your seed trays or garden beds and find the strongest, tallest seedlings. Take note of the recommended spacing for the plant and then begin thinning out the weaklings.

Use thin scissors to cut the weak sprouts at the base and remove them. Seedlings like chard, kale, and lettuce are yummy to just pop in your mouth like microgreens!

You can also pull seedlings out with your hands, but you need to have very nimble fingers and ensure that you don’t dislodge the seedlings you want to keep growing.

The best time to thin is when seedlings are 2-3” tall, right after they develop their first set of leaves. I like to wait until the seedlings get past the cotyledon stage so I can properly assess which ones are the strongest. But, if you forget to catch them at the infant stage—late is better than never!

Overseeding and Overcrowding

Close-up of young tomato sprouts in starting trays. Tomato sprouts consist of thin stems and a pair of tiny, oval, pale green leaves. The soil is wet. Each cell contains three germinated seeds.
Take care not to overcrowd the seeds in one hole so that they do not interfere with each other’s germination.

It is a common misconception that planting extra seeds will result in extra yield. This is not usually the case with vegetable gardening. When there are too many plants crowded together, all of them suffer.

For example, broccoli is a space-demanding crop that prefers 12-18” of space in each direction. If you transplant five broccoli seedlings at 6” spacing, none of them will be able to reach maturity or grow a full head.

On the flip side, if you plant two broccoli plants at proper spacing, both of them can grow big central heads and may even send out lateral shoots later in the season.

How to Avoid It

Plan your garden in advance based on what you like to eat throughout the season. Order a little more seed than you think you need. When it’s time to plant, take care to count your seeds as they go into the soil. They don’t need to be perfect, but you don’t want to dump a bunch of seeds in one place, either.

If you’re having a hard time singling out tiny seeds like basil or lettuce, consider using a mini seed sower. Simply load the seeds into the round part of the dispenser. Then turn the wheel until you find an outlet that is small enough to release just 1-2 seeds at a time. Hold the pointed end over your seedling tray and gently tap the top to sow the seeds.

Pro Tip: For most vegetables, you can plant 2-3 seeds to ensure germination. When they sprout, you can thin to 1 seed per cell (if transplanting) or per hole (if direct seeding). The main exceptions to this rule are vegetables that are harvested in bundles, such as:

  • Scallions/Green Onions: 4-6 seeds per cell
  • Beets: 2-3 seeds per cell
  • Radishes: 2-3 seeds per cell
  • Baby Lettuce: 4-6 seeds per inch in rows 2” apart
  • Carrots (direct seed only): Evenly space about 1-2” apart in 2” wide bands, rows 12-24” apart

While some gardeners get overzealous with seeding, there are a few that actually under-seed. You want to be sure you have enough plants to make up for any unexpected events like weather, damping off, rodents, or poor germination.

Forgetting to Label and Date

Top view, close-up of female hands signing labels for seeds. On the table, there are two starter trays for sowing seeds with soil, a package of parsley seeds, a green spatula and a bowl with white, long labels for signing seeds. On one of the labels, it says "Salad" and on another, the girl writes the word "Basil".
Use variety labels and dates on your seeds, as many seedlings look the same and will be easier to tell apart.

Without variety labels and dates on your seeds, how will you know what the heck you planted? At the time of seeding, we always tell ourselves, “I’ll remember what this is.” Guess what? You seldom remember 3-5 weeks down the line when spring is in full swing!

With a small garden, it may seem easy to differentiate between kale and broccoli, but the seedlings look surprisingly similar. Moreover, if you are growing multiple varieties of a crop that can cross-pollinate (like zucchini and yellow squash), you will want to have them labeled so that you can plant them separately in the garden.

Another bonus of labeling is that it makes you a better gardener! You have more references for next year. If you see that one cultivar is performing better than another, you can take note and order only the best variety next year.

Dating your seeds will help you plan your garden for more success next year. This is especially important for succession planting (when you sow the same crop every couple of weeks for a continuous supply).

How to Avoid It

Use popsicle sticks and a permanent marker to label every single seed tray or seed bed. On the popsicle stick, write:

Variety Name

Write the variety name on a tag when starting seeds. Use abbreviations if necessary due to the variety. For example, ‘Black Magic’ and ‘Red Russian’ are two types of kale.

I know they are kale, so I don’t need to write that on the stick. I may abbreviate “B. Magic” and “R. Russ” to remind myself which is which and when they were planted.

Date of Seeding

This will make it so much easier to track your garden’s success and optimize the germination rate of your veggies. If you seeded head lettuce on 2/10 and notice that it hasn’t emerged by 2/25, you know something was wrong with the seeds or your planting method.

Lettuce usually germinates in 7-10 days. You will want to re-seed immediately to ensure you have lettuce ready to plant for spring salads.

Face all your popsicle sticks in the same direction for easy reference. Don’t use a pen or pencil— they just wipe off or fade when you water.

Seeding At the Wrong Time

Close-up of a farmer's hand planting seeds in the soil. The seeds are small, round and brown. The soil is loose and dark brown in color.
Make sure you sow the seeds neither too early nor too late for a good harvest.

If you start seeds indoors too early, the plants may overgrow their containers before it is warm enough to get them outside. But if you start seeds too late, your climate may not provide enough frost-free days for the crop to mature.

If you direct sow in your garden too early, an unexpected spring cold front could wipe out your planting. Similarly, if you sow too late into the fall, your crops may not have time to mature before the winter frost arrives.

On the other hand, if you seed lettuce or cilantro in the heat of summer, it will likely bolt before you can get a good harvest. Needless to say, timing is everything!

How to Avoid It

It is important to study the days to maturity of each variety and create a calendar based on your seeding dates. A seeding journal can help you track the seed dates from year to year.

If I know that I planted sugar snap peas on March 1st last year and they thrived, I can seed on the same day this year. If last year’s records remind me that my tomatoes were rootbound at the time of transplanting due to a late spring frost, I might want to push my seeding date back a week or two this year.

Record-keeping isn’t just for farmers and accountants! It’s for savvy gardeners like you who want to optimize their yields and grow the highest quality food possible!

Use the Farmer’s Almanac to identify your last frost date and use that as your “north star” of seed planning. Most growing guides and seed catalogs will recommend a time frame for seeding indoors (for transplanting) and outdoors (for direct seeding). This time frame will be based on the frost date and the length of time the seedlings need to develop.

Burying Seeds Too Deep

Close-up of a gardener's hands sowing seeds into starter seed trays filled with soil in a garden. Seeds are small, round, orange-pink.
The depth of seed placement is important, it is desirable to sow them to a depth twice the width of the seed.

Seeds need to be buried at specific depths. When you bury a seed too deep, it dramatically reduces the rate of germination success. This mistake is especially common with small-seeded crops like lettuce, celery, poppies, basil, thyme, tomato, arugula, cabbage, fennel, oregano, etc.

Think of a seed like a little baby in a package with some food. If you plant the seed too deep, it won’t have enough energy to reach the surface. To understand this better, here is a simplified explanation of the biology of a seed. A seed is made up of three main parts:

Seed Coat

The outer protective packaging of the seed makes it possible for the seed to withstand storage and transport. For most vegetables, water is usually enough to dissolve the seed coat and trigger germination.


This is the starchy “food” source that helps the seed sprout. This is only enough energy to fuel the seedling until it grows up to the surface of the soil. Then, it will develop cotyledons (the earliest leaves) and start photosynthesizing.


This is the “baby” that will grow into a new plant.

For a large seed like cucumber or pumpkin, sowing ½” to ¾” deep in the soil isn’t as big of a deal because the seed has a lot of food reserves. The endosperm will fuel the baby plant all the way up to the surface, where it can then sprout leaves and start making its own food via photosynthesis.

However, a small seed planted too deep can die on its journey up through the soil, or it can rot in the depths of a soggy pot.

How to Avoid It

Most seed packets include a recommended planting depth. But you can also use this secret trick for determining seed planting depth.

Seed Depth Rule of Thumb: Plant a seed twice as deep as the seed is wide. In other words, never sow a seed any deeper than twice its diameter.

For example, if a bean seed is about ½” wide, you want to plant it 1” deep. However, a tiny rounded kale seed may only be 2mm wide. It should be planted about ¼” deep.

Of course, the rule isn’t designed to be ultra-precise. You don’t have to use a ruler or magnifying glass to figure this out. Simply use your best judgment and create a “dibble” hole that is sized based on the seed.

Letting Seeds Dry Out

Close-up of a gardener's hand testing the soil of freshly planted seeds in seed trays, on a table. There are also pots with bags of different seeds on the table. A gardener in a colorful sweater.
Check freshly planted seeds every day by touching the soil to ensure they are properly watered.

Like any baby organism, a plant is most needy during its germination stage. If your seeds don’t remain consistently moist, they will dry out and die. Freshly started seeds need to be checked every 1-2 days. The seed-starting season is not the time to go out of town!

How to Avoid It

Maintain consistent moisture so that seeds never dry out, nor do they sit in soggy soil. Check your seed trays every day and touch the soil. If you can, stick your finger into the soil. If your skin comes out clean, it’s probably too dry.

Also, notice the color and texture changes based on your seed-starting mix. If the soil is pale and brittle, you need to water your seedlings immediately. If it looks like soggy chocolate pudding, reference the next mistake…

Overwatering Seeds

Close-up of a watering can watering trays with germinating seeds, in a garden, against a blurred background. Large plastic black tray, with round holes filled with moist soil. The sprouts are tiny, have thin stems and a pair of oval bright green leaves.
Over-watering can cause seed rot.

Water is clearly essential for healthy plant growth, but sometimes you can give too much of a good thing! Overwatering can quickly destroy your seeding efforts by welcoming pathogens into the planting environment.

Seeds easily rot in their trays (or in the ground) when they are sitting in too much water. If your seeds have already germinated, saturated seedling mix causes a lack of oxygen in the root zone, resulting in root rot or damping off.

How to Avoid It

If you notice mold or algae growing on the surface of your soil, you are overwatering. Stop watering immediately and move the seed tray to an area with warm, bright light.

Allow the soil to dry out partially and assess if the seedlings still seem strong enough. If not, you will want to discard any soil that could be contaminated with fungal pathogens, then get a fresh start on your seeds.

To ensure the proper amount of water, always do a test run first. Sprinkle water (using the methods below) over the surface of the seeds or seedlings and allow it to run through.

If the water pools up, the soil is already too wet, or you are using a poorly drained seed-starter mix. The water should run through the soil and drain out of the bottom into a catchment tray.

Use several passes of your hose or watering can ensure that water doesn’t pool up in one area. Once the water comes out of the drainage holes, stop watering. Depending on the cell size, soil texture, humidity, light, and temperature, you may need to water again in 1-3 days.

Key Caveat: “Overwatering” refers to giving seeds too much water. Please don’t confuse this with “overhead watering,” which means watering seeds from above. As you’ll see below, irrigating from 1-2 feet above freshly sowed seeds is ideal.

Dislodging Seeds with Intense Watering

Close-up of spraying freshly planted seeds into square mesh trays. The tray is plastic, black, with blue cells filled with moist soil.
With improper watering, your seeds may float to the surface or move to the other side of the cell.

Improper watering can quickly sabotage your seeding efforts. If you just took all the extra time to plant your seeds at the proper depth and spacing, you probably don’t want to ruin your hard work with a blast of water.

Beginners often think that they can just dump a watering can or a high-flow hose over the top of their seed trays. This can quickly oversaturate your soil and leave seeds floating around on the surface. The result? Poor germination, more thinning work, and seeds that germinate in weird spots (like the corner of a cell rather than the middle).

How to Avoid It

This is most important in a nursery, greenhouse, or indoor seed-starting setup, but these guidelines can be applied to outdoor watering as well. There are three main ways to prevent this mistake:

A quality hose nozzle

Invest in a fan hose nozzle that spreads irrigation water out in an even “sprinkle” rather than a heavy blast. Hold the hose at least a couple of feet up above the seeding tray, and never hold it in one place for too long.

Keep your hose continuously moving back and forth over the seed trays until they are moist. The same method applies to seeds outside in your garden beds. Imagine light rainfall, not a dump bucket.

Quality watering can

If you are seed starting in your home, you can achieve a similar effect with a high-quality watering can. Look for a top that has a fan-like nozzle rather than a big pour spout.

You want the water to sprinkle out rather than pour into one space. Gently sprinkle water over your seeds and keep the watering can moving. Better yet, bring your seed trays onto a patio and water them from above before bringing them back inside.

Bottom watering

Indoor growers may also prefer bottom watering. It is less messy and ensures that seeds don’t get dislodged. Simply place your seed trays (the ones with drainage holes) inside a solid bottom.

Add about an inch of water to the tray and let the soil soak it up from the bottom to the top. Capillary action allows the soil and seedling roots to suck the water up from the drainage holes. This same method is used for potted plants that are placed in saucer trays.

Growing in Low Lighting

Close-up of young plant seedlings growing in a germination tray, on a light windowsill with potted plants. Sprouts have long thin pale green stems and 2-3 round, bright green leaves.
Give your seeds at least 6 hours of bright sunlight to germinate.

Most garden seeds require a minimum of 6 hours of bright sunlight to properly germinate and grow. When seedlings don’t get enough light, they become leggy and weak.

They are reaching up to get more sunlight instead of channeling their energy into strong roots and new leaves. You will know that your seeds need more sunlight (or grow lamps) if they appear pale, spindly, and have elongated stems.

How to Avoid It

Only plant seeds in areas with ample sunlight for the crop species. If you are growing seeds indoors, keep the grow lights low so that the seed trays stay about 10-12” beneath the light to prevent legginess.

If you are growing on a windowsill, be sure that it is south-facing and doesn’t have anything blocking the sunlight. When growing in a greenhouse, make sure there aren’t any trees or larger seedlings around to shade out the developing seeds.

Creating Conditions for Damping Off

Close-up of a male hand holding a young physalis seedling growing in a special propagation pot. The sprouts have small, thin, hairy stems with three round leaves.
Make sure there is adequate airflow, use a well-drained potting mix, and avoid overwatering.

Damping off is a fungal disease that specifically attacks baby seedlings (how cruel!) It thrives in conditions where:

  • The air is stagnant (not enough airflow or wind)
  • The plants are overcrowded (due to over planting or a lack of thinning)
  • There is an excessive amount of moisture in the soil.

As soon as a seed germinates, the pathogen attacks the seed from the base, often leading to a girdled stem and a collapsed seedling. Sometimes the seedling stem will hang on by a shoestring and start to turn white right near the soil surface.

How to Avoid It

Once damping off takes hold, most seedlings can’t be saved. Prevention is key.

Remember The Following
  • Use fresh seed-starter mix for every new seedling.
  • Don’t re-use garden soil or old potting mix.
  • Use a very well-drained soil blend.
  • Avoid overwatering.
  • Check that your pots or seed trays have good drainage holes.
  • Use a fan in your home or greenhouse to ensure airflow.
  • Don’t overcrowd plants.

Selecting the Wrong Seed Mix

Top view, close-up of female hands pouring soil into the cells of the sowing trays. The soil is dark brown and loose. Plastic trays, white, with round holes.
It is recommended to use a seed-starting mix.

Your seed starting mix is the foundation of your entire gardening season. It is worth the investment to buy a high-quality soil mix such as:

  • Espoma Organic Seed Starter Mix
  • Black Gold Organic Seedling Mix
  • Burpee Organic Seed Starting Mix
  • MiracleGro Seed Starting Potting Mix

Note that these mixes are specifically designed for starting seeds. They will have the term “seed starter mix” somewhere on the package. If you are growing organically, you will also want to look for the OMRI seal, which verifies the product is approved for organic gardening and farming by the Organic Materials Review Institute.

Seed-starting mixes are different from standard potting soil because they are formulated to provide the best environment for germinating seeds. Sometimes seed-starting blends can be used as potting soil, but the opposite is not recommended.

Seed-starting mixes have lots of aerating materials like peat moss, vermiculite or perlite. Oftentimes, seed starting mixes are “soil-less,” which means they don’t have real garden soil in them. This ensures that the mix is sterile and pathogens won’t contaminate the seedlings.

How to Avoid It

Beginners will see the best results using a store-bought seed starting mix. These blends are fairly affordable and ready to go straight into your seed trays. However, you can make your own mix with the following guidelines.

For vegetables, try a ratio of 2 parts compost to 2 parts peat moss to 1 part perlite to 1 part vermiculite. Thoroughly blend together and chop up any chunks with a shovel.

If you are using compost from your garden, be sure that it has thoroughly aged, cooled, and sieved to get out any large chunks.

Always pre-wet seedling mixes that have peat moss or coco coir in them. These materials are highly hydrophobic (they repel water) and need to be rehydrated to ensure that the mix stays evenly moist after you sow the seeds.

For dry soil herbs and cuttings (like lavender or rosemary), use a mix high in horticultural sand for optimal drainage.

Bonus Tips For Seeding Mixes

  • Never seed in bone-dry seedling mix, but also avoid soggy mixes.
  • Find a happy medium of moisture before sowing your seeds.
  • Avoid using potting soil that may be contaminated with pathogens.

Bonus Tips For Direct Sowing Outdoors

  • Incorporating compost in advance.
  • Lightly hoeing the top few inches of soil.
  • Removing any large rocks or clumps.
  • Raking the soil into a fine flat surface.
  • Using a “Zipper” hoe or the back of a garden tool to make a furrow.

Final Thoughts

Starting seeds in your garden doesn’t have to be a difficult task. You just need a bit of preparation and some patience. The secrets to thriving seeds can be summed up by the following:

  • Thin your seedlings based on the proper spacing for the plant.
  • Don’t plant too early or too late.
  • Avoid underwatering or overwatering.
  • Sow seeds in a place where they can get plenty of light.
  • Choose a high-quality, well-drained soil blend for seed-starting..

If you follow the guidance provided above, you should be off to a fantastic start in your garden this season!

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