12 Seed Germinating Issues & How To Fix Them

Troubleshooting Seed Starting Problems and How To Fix Them

Growing your own food and flowers can be very satisfying, but if you are struggling with getting your seeds to germinate, it can also be very frustrating. There are a few mistakes that first time gardeners, and even experienced growers, may make while starting seeds. The most common issues are:

Incorrect Lighting
Low Soil Temperatures
High Soil Temperatures
Incorrect Seeding Depth
Inadequate Moisture
Too Much Moisture
Too Little Oxygen From Compacted Soil
Estimated Germination Window Hasn't Ended
Seeds Stored Incorrectly or Seeds Were Old
Pest/Rodent Problems
Fertilizer Needs
Naturally Low Germination Rate

Reason #1: Incorrect Lighting

Some seeds require light to germinate while others require darkness to germinate. Read the packaging carefully for each variety of seeds. Seed that require light to germinate SHOULD NOT be covered with soil or vermiculite. Seeds that require light to germinate should be sown on the surface of your pre-moistened soil mixture. Seeds that require dark to germinate SHOULD be lightly covered with either soil or vermiculite.

Once your seeds have germinated, you'll want to make sure they have adequate light to grow properly. Young plants that receive insufficient light will become leggy (i.e. have long, pale, thin stems) and develop weak stems. This can lead to serious issues when transplanting and can also cause plants to be more susceptible to disease. The easiest way to avoid this is by using artificial light. Grow lights and light stands allow you to adjust the height of the light to meet each of your plants needs as they grow. Automatic timers make it easy- set the timers to turn on and off when you want them to every day. Find a large selection of different light stands and grow light fixtures here.

Reason #2: Low Soil Temperatures for Germination

In addition to needing adequate moisture and either light or dark to germinate, many seeds also like to be kept at a specific temperature to maximize their rate of germination. The temperature needed for germination for each seed can be found on their packaging. Please note that when germinating seeds indoors, the soil temperature is often 5° F cooler than the ambient/room temperature. If a seed variety requires a soil temp. of 70° F, a room temperature of 70° F will most likely not be warm enough for germination. Heat mats are an easy way to help maintain the proper soil temperature. Most heat mats come with a temperature probe that can be placed in a pot or one of the cells in your plant tray and will allow the heat mat to maintain a steady temperature. If you are starting three or four different types of seeds, all with their own temperature guidelines, don’t worry! Simply choose a mid-point temperature that is within the range of the seeds. For example, if one variety of seeds should be kept at 70-85° F, but the other three should be kept at 65-75° F, simply set your heat mat to 70° F. This will be adequate to cover the needs of all your seeds.

Heat Mat for Germinating Seeds

Reason #3 High Soil Temperatures for Germination

On the flip side you don’t want to cook your seeds. Most seeds do not do well in temperatures over 80° F. If using a heat mat, make sure you adjust the temperature control to the correct setting. If planting directly in beds (in a greenhouse or outside) it might be worth investing in a soil thermometer which will help you identify the temperature of your beds. Some crops like spinach and lettuce do best started at cooler temperatures while crops like tomatoes, peppers and eggplant thrive in warmer temperatures.

Soil Thermometer

Reason #4: Incorrect Seeding Depth

Pay close attention to the seed starting depth that is indicated on the packaging. Most seeds are small and should not be buried deeply. If you bury the seeds too deeply, they won’t have the energy necessary after sprouting from their seed hull to push through the soil and reach the surface. A general rule of thumb is that seeds want to be planted at a depth only 2x the diameter (width) of the seed. If you are seeding by hand, ere on the side of caution and take care not to bury the seeds too deeply. If you are using a tool to sow seeds mechanically, make sure you adjust the seeding depth and set it at the appropriate level for the variety of seeds you are sowing. Earthway and Jang seeders come with instructions on setting the seed depth as well as a variety of seed plates for different size seeds. Pay close attention to the instructions and adjust accordingly.

Reason #5: Inadequate Moisture

Seeds must be kept moist to germinate. It is very important that they do not dry out once the seeds start to germinate. This is especially true for pelleted seeds. Pelleted seeds are covered in a fine coating of talc or clay powder mixed with a sticking agent. If this mixture dries out at all during the germination process, it turns into a very hard coating and makes it nearly impossible for the seed inside to germinate and emerge. A very easy technique is to pre-moisten your seed starting mix or soil prior to seeding. This will greatly improve your germination rates. To help maintain adequate soil moisture levels after sowing your seeds, use a plastic dome to cover your trays or pots. Water with a spray bottle or a misting head on your hose to avoid disturbing the soil and your seeds. Once the seeds have germinated and the plants have emerged from the soil, you can remove the plastic dome as you see fit.

A note about pelleted and multi-pelleted seed:
Germination issues are common when moisture levels are not properly maintained. Water management for multi-pelleted seed is similar to that of a clay pellet. The water-soluble wax of these pellets takes longer to completely dissolve even when fully submerged in water. Do not attempt to dissolve the pellet within a single watering. Instead, maintain a moisture level of four to five (medium wet to saturated) from sowing until the pellet is fully dissolved. The use of plastic domes or regular misting is helpful in keeping the adequate moisture until the seed germinates. Once the sowing stage begins, if the pellets dry out, they become hard to dissolve.

Pelleted Seed & Plant Tray with Plastic Humidity Dome

Reason #6: Too Much Moisture

Take care not to overwater your seeds. If you see algae growing on the surface of your soil you are overwatering and may be in danger of rotting your seeds. If you are using a plastic dome, remove the dome or prop the side up to allow for increased air flow. Wait to water until the soil has dried out a bit. Too much moisture can lead to fungal issues and often to something called, damping off. Damping off is caused by soil borne fungi that negatively affect seeds and young seedlings and cause the root system to rot. It can affect all types of plants.

Reason #7: Too little oxygen from compacted soil

If your soil is heavy and compacted, your seeds are not able to properly absorb oxygen and water, and may fail to germinate. Be sure to use a well-aerated seed starting mix. In addition, once your seeds germinate, the young plants require a broad range of nutrients in order to grow. Nutrient uptake is a delicate balance governed by oxygen and moisture levels in the soil and the ability of a plant’s roots to access these molecules. When direct sowing crops outside, consider using a tiller or a broad fork to help aerate the soil prior to sowing seeds. The method you use may depend on the scale of your grow operation. If your operation is largely mechanized, you may struggle with soil compaction and the development of a “hard pan.” Remember to incorporate cover crops into your crop rotation. Cover crops can improve soil structure and stability, increase levels of organic matter in the soil, and over time, can improve the soil’s moisture and nutrient holding ability. In addition, crop rotation is critical for reducing the level of pathogens in the soil and pest population.

Reason #8: Estimated germination window hasn't ended yet

Most crops will germinate within about a week of sowing. Many will germinate in just a few days. However, there are a few types of herbs and flowers that are slow to germinate and may require 2-3 weeks to germinate (ex: parsley, celery/celeriac, petunias, lavender, rosemary, etc). The time needed to germinate for each variety of seed can be found on the seed package. If you are working with herb or flower seeds that take a long time to germinate, be patient! Continue to water them and provide them with the necessary warmth, light/darkness and monitor for growth.

Lavender & Rosemary from seed

Reason #9: Seeds were stored incorrectly or seeds were old

Most seeds can last well over a year if they are stored correctly (some can last for years!), but they all have a basic life expectancy. As seeds age, their germination rates will begin to slowly decline. Here at Harris Seeds we store our seeds in optimal conditions and test our vegetable seeds every 6 months and our ornamental seeds every 9 months, to guarantee that our customers receive the very best seeds with the highest germination rates. We recommend that seeds are stored in a dry, cool location where they are not subject to changes in temperature or humidity. This will maximize the life span of the seeds you have purchased.

Reason #10: Pest/Rodent Issues

Whether you are starting seeds indoors, in a greenhouse, or direct seeding outside, pests and rodents can be a huge issue. Mouse traps and sticky traps can help in a controlled environment (inside or in your greenhouse) but are of limited use outside. If you are having issues outside, consider investing in fencing around the perimeter of your grow space to keep out larger animals and in row covers to protect young plant starts. Row covers can be used on direct seeded crops and transplanted crops. They will provide some protection from birds and insects, and they are also a great way to provide some season extension in the early spring and in late fall!

Yellow Sticky Traps & Fencing

Reason #11: Fertilizer Needs

All crops need a healthy balance of nutrients to grow and depend on the soil to provide this mix. Prior to planting your beds, have a soil test done to determine what your soil may need. We offer a variety of different soil test kits. Before adding any amendments, make sure you understand what your soil needs and when to add fertilizer or compost. Compost must age before it is added directly to your garden beds or it will be too “hot” and can burn the tender roots of your young plants or seeds that are trying to germinate. In addition, some types of fertilizers need time to break down before they become available to your plants. Take some time to research what your soil needs, what the individual needs are of the plants you want to grow, and what the best methods are for providing them with these nutrients. Some fertilizers are designed to be added to the soil prior to planting, some can be added to an irrigation system and still others are best used midseason as a supplement to maintain growth and fruiting. A full list of the fertilizers and application tools can be found here.

Soil Test Kits

Reason #12: The seed has a naturally low germination rate

Remember that all seeds have different germination rates. This information can be found on our seed packets and will provide you with a guideline for what to expect from your seed. Some seed varieties have naturally lower germination rates. Some examples include: Canna, Echinops, Larkspur, Huechera, and even some Impatiens. By purchasing seed from a reputable seed company (like Harris Seeds!) you are taking some of the guesswork out of the equation. We source high quality seeds that are disease free and test our seeds onsite to make sure that the germination rates exceed the standards set by New York state.