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Starting your own seedlings indoors is a great way to get a head start on your gardening but growing strong and healthy plants from seed isn’t always an easy task.

There are several common seed starting problems that gardeners may face when growing seedlings indoors and most can be traced back to a few key issues, like overwatering, overheating, and overcrowding.

By tackling these frequent mistakes, you’re sure to grow strong and hardy plants that will produce delicious vegetables during harvest season.

Whether your seeds aren’t growing or your seedlings appear weak and feeble, I have you covered!

Together, we’ll dive into the most common seed starting problems, and I’ll give you some suggestions on how to fix them.

Common Seed Starting Problems and How to Fix Them:

Common Seed Starting Problems and how to Fix Them

Dampening Off

Sometimes, seedlings will appear to be growing strong, when suddenly they wither up and die.

This process is called dampening off, and it is one of the most common seed starting issues gardeners face. Luckily, there are a few ways you can prevent dampening off from ever happening.


Overwatering is the most common cause of dampening off.

When you water your seedlings too often, you allow disease to grow in the soil, causing the plants to mold.

To ensure that you do not overwater your seeds, only add water when the soil begins to dry out.

Watering from the bottom will also help you avoid adding too much water to your seedlings.

If you don’t know how to bottom water, this video is great about explaining how:


Another way to avoid this common seed starting problem is by planning ahead.

Before planting your seeds be sure your seed starting equipment is sterile by disinfecting all of your seed trays and pots before using them.


Choosing the right soil is also crucial. You should opt for a high-quality seed starting medium instead of regular potting soil and never reuse any of your soil for other seeds.

Common Seed Starting Problems

The Seeds Never Germinate

There are a few reasons a seed will fail to grow at all.

First, make sure your seeds aren’t too old. If seeds are not stored properly, the chances of them germinating are less likely. To properly store seeds, make sure they are in a cool, dry place.

Temperature and water are also contributing factors to whether your seeds will grow.

Just as different plants have different needs in the garden, different seeds need different things when growing indoors.

Cool weather crops (cabbage, cake, broccoli, etc.) require lower temperatures than warm weather crops (peppers, tomatoes, etc.).

Those warm-weather crops may require a heat source such as this one if you are growing them in a cool area (lower than 70 degrees Fahrenheit).

Watering requirements are another factor to consider. Most seeds need evenly moist soil – too much or too little water can cause growth problems, as well.

One final factor to consider if your seeds never germinate is the relationship between planting depth and light. Some seeds actually need light to germinate, so planting them too deep will force them to run out of energy before reaching the surface of the soil.

Discolored Leaves

Discolored or faded leaves means there is a problem that needs to be addressed quickly.

Most of the time, you can save your seedlings if the problem is remedied soon, but if the damage is too severe, the seedling may not survive.

Soil and watering issues are usually the cause of discolored leaves.

As I mentioned before, be sure to water your plants properly (preferably from the bottom) and choose a quality seed starting mix to ensure your seeds and seedlings are getting the nutrients they need.

Your seedlings may also be experiencing burning. Fertilizer burn came come from the use of harsh chemical fertilizer.

To alleviate this type of burn, switch to natural or organic fertilizers when feeding your seedlings.

Sunburn can also cause leaf discoloration. If you suspect sunburn is the issue, move your seedlings out of indirect sunlight immediately.

To avoid future sunburn, properly harden off your seedlings by placing them outdoors for a few hours each day in a shady location before placing them in direct sunlight.


Weak Seedlings

Sometimes seedlings will sprout but not grow. This a common problem that can be fixed fairly simply.

Most of the time, weak seedlings are the result of nutrient deficiencies, watering problems, or temperature issues.

If your soil lacks nutrients, your seedlings will not grow properly. There are a variety of nutrients your seedlings need to grow into strong and thriving plants, including nitrogen, calcium, magnesium, potassium, and phosphorus.

To keep your seedling’s soil nutrient-rich, feed your plants with an organic plant food by following directions on the product.

Just as watering and temperature were important when you planted your seeds, those elements must be regulated as your seedlings grow.

Warm weather crops need temperatures of around 75 degrees Fahrenheit to thrive.

Also, be sure you are not overwatering your seedlings. Too much water can prevent your seedlings’ roots from bringing in much-needed oxygen, which can stunt your plants’ growth.

Remember to water your plants only when the soil begins to dry out and add just enough water to moisten, not soak, the dirt.

Thin, Leggy Seedlings

Starting seedlings indoors often results in thin, leggy plants.

Most of the time, these leggy seedlings are the result of lighting issues and can be easily fixed.

One of the best ways to make your seedlings hardier is to take advantage of sunny days and allow your seedlings to take in some indirect sunlight.

Placing leggy seedings in a protected area outside will allow them to benefit from the sun, while also starting the hardening off process.

If the weather is still too cold to continually place your seedlings outside, try adding more lighting to your growing area.

A grow light helps mimic the sun’s rays and will provide additional warmth needed to help your seedlings thrive.

A sunny window is another great option for providing your leggy seedlings with more light. Be sure to rotate your planting trays throughout the day to ensure that each seedling is receiving an adequate amount of light.

To keep your seedlings from competing for light, it also helps to thin out your crowded trays as the time for transplanting grows near.

To do this, cut out the weakest seedlings at soil level so only one plant is growing per cell. Never pull the plant out of the soil, because you may risk pulling a hardier plant out along with it.

Larger seedlings should be transplanted into seedling pots to avoid continued overcrowding.

Bugs and Mold

While the presence of bugs and mold around your seedlings isn’t detrimental, you need to address the issues causing those problems to ensure you have a healthy crop.

Once these problems are under control, the bugs and mold will disappear as well.

Mold is usually caused by overwatering, overcrowding or a lack of air circulation.

To avoid overwatering, only water when the soil is dry and keep it moist, not soaked.

Overcrowding can be remedied by thinning our seedlings or transplanting them into larger seedling pots.

To increase air circulation in your growing area, add an oscillating fan to the room and allow it to blow over your seedlings. Not only will this increase air flow around your plants, but it will also help dry out soggy soil.

Overwatered plants can also attract soil gnats, which feed on rotting organic material like unhealthy seedling roots.

Watering your seedlings from the bottom will give your seedling’s soil a chance to dry out between watering.

To control the gnat problem as your plants dry, place yellow sticky traps near the plants to catch the flying bugs.

I hope this helps you out with any problems you are having while starting your seeds.

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