Germinating Seeds for Hydroponics

By Monica Mansfield
Published: May 17, 2021
Key Takeaways

Germinating seeds for hydroponics is simple and can result in stronger, happier plants in your garden.

If you have decided to grow a hydroponic garden, you may be wondering where to get plant starts and if it’s okay to use them if they are growing in soil. Unfortunately, this probably isn’t a good idea. It may be difficult to clean soil from the roots without stressing your plants, plus you’ll run the risk of introducing soil-borne pathogens into your system. When you have a hydroponic garden, take extra care to prevent diseases by only using clean starts. This means your best bet is to germinate your own seeds.

There are many things to consider when starting seeds for your hydro system. You’ll need to choose a location suitable for growing, gather your supplies, choose a medium, and prepare your seeds for planting. Once you figure out a game plan, germinating seeds is a pretty simple job.


Choose Your Germination Location

When you choose a location for seed starting, make sure the environment will be ideal for your seedlings. A warm spot inside your home such as an unused closet or in front of a south-facing window, or a growroom, grow tent, or greenhouse are all ideal options.

You will be playing the role of Mother Nature and are in control of monitoring and adjusting your environment. You need to choose a location that is about 74°F, with relative humidity between 40-60 percent. Your location will also need enough space for all your seedlings as they grow, plus equipment such as grow lights, a fan, and a dehumidifier.


Keep in mind the temperature will be affected by your grow lights, heat mats, and other equipment. Your humidity will be affected by the number of plants growing. The more equipment you have, the higher the temperature and the more humidity you potentially burn off. The more plants you have, the more moisture will be produced from transpiration and evaporation. You’ll need to adjust the different parts of your growing area to create an ideal environment.

Gather Your Seed Starting Supplies

In order to create this environment, you’ll need to gather some supplies. Fluorescent grow lights work well for seed starting, although you may need more powerful lights as your crops get older. A sunny window probably won’t produce enough light. Plug your grow lights into a timer to control when they turn on and off.


Seeds germinating inside a seedling tray.You’ll find seed trays available in a range of capacities to fit many different growing needs.
A heat mat and humidity dome or plastic wrap will help you keep your seed-starting medium moist and warm. If you want to control the exact temperature of your heat mat, you can buy a temperature controller, but I don’t find that is usually necessary. You’ll need a thermometer/hygrometer to monitor the temperature and humidity inside and outside the dome, a dehumidifier to maintain the proper humidity level, and an oscillating fan to create air flow, which keeps fungal diseases at bay and strengthens the young seedlings.

You’ll also need to gather trays, starter cubes, and, of course, the seeds you’ll be starting. Make sure your trays and domes are cleaned and sanitized in order to prevent disease from spreading through your garden.

Choose Your Grow Medium

Germinating seeds for your hydro system is a lot like starting seeds for any other garden. The main difference will be the growing medium you use. In a hydroponic system, it’s best not to use a loose medium and opt for a starter cube instead. This way you don’t contaminate your system and clog your emitters. Starter cubes are also easier to add to any system without stressing the plants.

Starter cubes are made out of many different types of materials, including stonewool (rockwool), peat moss, coconut coir, sponges, and foam. Each type of plug has pros and cons, but what is most important is that the plug can remain moist while having an air-to-water ratio that promotes root growth. Some plugs are treated with micronutrients or beneficial bacteria to jump start root growth from the very beginning. Others, like stonewool, need to be treated before use to adjust their pH.


Seedlings sprouting in a foam or sponge starter medium. Starter plant plugs provide just the right aeration and moisture control for the successful germination.
Once your seedling is a few inches tall and has its true leaves, you can easily place the cube into your hydro system without stressing your plants. Starter cubes are flexible and work well alone in net cups, in clay pellets or gravel, and in sterile soilless mixes.

Prepare Your Seeds for Germination

Different seeds have different requirements for seed starting. Some need to be soaked overnight or placed in the refrigerator for a couple of weeks prior to planting. Others need to be nicked or scratched to allow the plant to escape the seed pod.

Get to know the seeds you’ll be growing and how to grow each kind of crop. You’ll also need to understand the timelines for your plants and plan your indoor garden accordingly. Grow plants with similar growing requirements together. If they grow in your outdoor garden at the same time, chances are they will grow well together indoors too.

(Read also: Growing Up Together: The Science Behind Companion Planting)

You may want to check your seeds’ viability before planting, especially if your seeds are a few years old. Seeds can last from one to five years or longer, depending how well they were stored. To test your seeds, place 10 or more seeds in a wet paper towel, in a closed plastic bag, and place the bag in a warm location. If only a couple of your seeds germinate, they probably aren’t worth the effort and you should invest in a new packet of seeds.

Plant Your Seeds

Before planting, prepare your starter cubes by soaking them in distilled water for a couple of hours and then drain the water. To plant your seeds, place two to three seeds in the hole on top of the starter cube and then cover. The general rule of thumb is to plant seeds as deep as they are long. Some very small seeds, such as celery and dill, should be surface sown because they need light to germinate. Keep your medium warm and moist by covering your tray with a dome or plastic wrap and then place it on a heat mat.

Most seeds germinate between 65-75℉, however, each seed has its own ideal temperature. If the soil temperature isn’t right, it can take longer for seeds to germinate, or they may not pop at all. For example, peppers will germinate in eight days at 86℉, but take almost two weeks at 58℉. Eggplants, melons, pumpkins, squashes, and tomatoes all have optimum soil temperatures between 80-95℉. You can adjust the soil temperature with a heat mat and temperature controller and monitor your results with a soil thermometer.

Once they break through the soil, the seeds will also need the environment to be the correct temperature, which is different for different plants. You may need to plan to germinate cool-weather and warm-weather crops at different times for best results.

Grower transplanting a seedling into a hydro system.Once your plant is a few inches tall, has a few leaves, and has healthy roots growing out of the cube, you can place the seedling into your hydro system.

Care for Your Germinated Seedlings

Once your seedling appears, you can gradually remove the dome or plastic wrap to lower the humidity directly around them. Each type of plant has its own preferences for humidity, but in general the humidity level should be higher during the seedling and vegetative stages.

Be sure to water your seedlings on a regular basis but be gentle. You can use a spray bottle to mist the soil, or water from the bottom so you don’t disrupt the tiny roots. You don’t want your starts to dry out, but you also don’t want them to be too wet to breathe. Once the true leaves appear, start adding a quarter- to half-strength fertilizer to your water.

Position the fluorescent grow lights a couple of inches above your seedlings and turn them on 16-24 hours per day. Fluorescents are not strong enough to burn your plants when they are this close. However, if you raise your lights too high, your seedlings may get leggy as they stretch to reach the light. If you do schedule your lights to turn off at night, keep in mind that will lower the temperature in the room, which may or may not be okay for the plants you’re growing.

(Read also: Leggy Seedlings: Too Much Leg Can Be A Bad Thing)

Soon you’ll see roots start to pop out from the bottom and sides of the starter cube. Once your plant is a few inches tall, has a few leaves, and has healthy roots growing out of the cube, you can place the seedling into your hydro system.

I like to treat my seedlings with a preventative neem oil treatment before adding them to my growroom. Pests are especially hard to eradicate indoors and preventing them is much easier than treating an infestation.

Once you get the basics down, it is easy and rewarding to germinate seeds for your hydroponics system. Your plants will be cleaner, healthier, and experience less stress at transplant time, which means you’ll have a happier garden right from the beginning.


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Written by Monica Mansfield | Homesteader, Owner & Writer of The Nature Life Project

Profile Picture of Monica Mansfield

Monica Mansfield is passionate about gardening, sustainable living, and holistic health. After owning an indoor garden store for 5 1/2 years, Monica sold the business and started a 6.5-acre homestead with her husband, Owen. She writes about gardening and health, as well as her homestead adventures on her blog at

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