Starting Seedlings in Hydroponics
By: Peggy Bradley

Some textbooks and manuals on hydroponics mention germination of seeds and recommend starting the seeds in soil. Nothing could be further from the truth.

Hydroponics is an excellent technology for germinating most types of seeds. Because there is no soil, many of the common diseases for seedlings are avoided in hydroponic culture. This includes a terrible disease called damping off, where the stem of the seedling dries up brown and then dies. This is usually caused by fungus in the soil, fungus that is not in hydroponic growing media.

A second disease of seedlings is root rot, caused by poor drainage in the seedling growing container. This can also be avoided in hydroponic culture.

While ordinary soil based germination in nursery businesses in the US expects a 70% germination rate, hydroponics can reach 90% to 95%.

Hydroponic culture can also modify the nutrient formula for the plant, creating a better growing environment for the young seedling. Specifically, a higher phosphorous compound encourages more root growth, at the expense of green growth above ground. The seedlings with excellent root growth are far more likely to transplant successfully.

It is for these reasons that many of the top growing companies have switched to specialized hydroponic systems to germinate their plants. One of the worlds largest timber companies reportedly grows almost all of its seedlings in hydroponic culture. They get better results, better plants, and they remove potential for many diseases. These tree seedlings are then planted in soil with excellent survival rates. So hydroponic plants can be transplanted into soil.

The advise to start seeds in soil is not correct in a hydroponic growing facility. It makes more sense to keep everything in sterile hydroponic culture and avoid the diseases and problems associated with soil.

The Germination Process

A seed is alive, breathing in oxygen and respiring carbon dioxide. While the seed is dormant, or not germinating, this rate of respiration is very slow.

When the seed is placed in an appropriate environmental conditions it will begin the process of germination. In this process with enough water and the correct temperature, (between 65 and 85 degrees F), the seed will start to germinate.

Most seeds have inhibitors within them that prevent germination. In many cases these inhibitors are water soluble so the inhibitors will break down in water allowing the seeds germinate.

A germinating seed breathes more rapidly than the dormant seed. It requires oxygen and respires carbon dioxide in order to grow. During this stage the seed needs to be in an environment which provides both oxygen and water to the seed.

This means an ideal environment for seed germination is one that allows the seed to have adequate oxygen and water such as a fluffy or air filled media appropriate for hydroponics. Mediums used for germinating seed have a high water-holding capacity, good drainage and aeration. A mixture of peat moss and builder’s sand in a 1:1 volume is commonly used in nurseries. Other growing media such as shredded sphagnum moss, vermiculite and perlite are also used for germinating seeds.

Setting Up Hydroponic Seed Germination


Grodan, Oasis and other rockwool companies manufacture 1" or 1.5" rockwool cubes especially designed for germinating seeds. These cubes come in sheets of 100 or more and can be placed in a bath of water and then a single seed placed inside the rockwool cube. This system is a tried and true method of starting seeds for the tomato industry. And this is important where some of the hydroponic tomato plants from Israel and Holland cost up to 75 cents for a single seed. Germination rates of 90% or higher are recorded using this rockwool method.

Most seeds of about 100 cubes are about 10 by 20 inches. The sheet is placed in a 10 by 20 inch growing tray, and the entire sheet is watered with a hydroponic nutrient. The water level should be only half the height of the rockwool cube or even a little lower. If the water level is too high the seeds in the cubes will drown in the excess water. The seed should be at a height where the water wicks up to the seed so air is available to the seed.

The rockwool method works very well when transplanting the small cube into a larger rockwool growing cube for the plant’s adult life. This is a commonly used method in commercial hydroponic culture for tomatoes and other vine crops.

Perlite Seeding Grower

A simple homemade grower can be made from a plastic tub or a wood carton lined in black plastic. The container should be about one foot by two foot surface area and at least six inches in depth. A plastic tub should be opaque or not let light through to the roots of the plants. If a clear plastic is used it will fill with algae and rob the seedlings of nutrients.

A wooden crate can also be adapted to be a seedling grower. A sheet of black plastic six mil in thickness or stronger, is placed in the container and stapled to the edge of the carton.

The container should have a drain hole placed about one inch from the bottom of the growing container. This allows any excess water to drain out of the planting area but still retains at least an inch of nutrient water in the bottom of the grower for young plants to have adequate water supply as they grow.

The tub or carton is then filled with perlite, a white porous growing material. Other materials can be used, such as coco fiber, vermiculite, or lava rock. However, perlite makes an excellent growing media for seedlings because it wicks water well, provides adequate air space and does not change the pH of the system.

Perlite is a volcanic material that has been mined and then popped in a kiln. This allows the particles to expand so they better hold both moisture and air. Because it is a mineral material popped in a kiln, it should be sterile the first time it is used.

Perlite can be purchased at a hydroponics store, or at most garden supplies. Make sure it is propagation grade which is pea gravel sized particles. There is also a building material available which is called masonry grade. This fine powder floats, so it does not make a good hydroponic growing media.

Seeds are planted in the perlite media exactly as they are planted in soil, usually from half to an inch deep.  As a general rule the seed should be planted no deeper than one to two times their diameter. Small seeds can be scattered over the surface or planted in rows and covered with a thin layer of media, just enough to keep them moist. The maximum depth for any seed is from two to three inches.

Some seeds such as lettuce can be sown on the surface of soil, but in hydroponics we plant lettuce seeds in rows about a half inch deep. This preserves the moisture area around the seed so that it will germinate.

Watering With Nutrient Water

After the seeds are planted they should be watered once a day with nutrient water. There are a variety of opinions on the strength of the nutrient water. Many seeds have stored nutrients in their tissues and do not need any additional hydroponic nutrients until they are fully sprouted. Other seeds such as orchid are very small and have almost no stored minerals.

As a general rule, in production of hydroponic seed starting, we start the plants out with a nutrient drenched media and add nutrient water every day. This is usually a nutrient that is mixed half strength to the nutrient that will be used in more mature plants. Thus the hydroponic nutrient is mixed at half the strength recommended by the manufacturer. This is kept until the seedlings are about two to three inches tall and ready for transplant.

Once the grower is set up, the entire growing medias should be watered down with hydroponic nutrient, seeds are planted and then planted seeds are rewatered every day.

Because the seeds are very small they can wash out of the growing container if the watering is too intense. Even when using a watering can, it is good to hold your hand in the watering stream and soften the impact of the water stream on the growing surface.

Some Seeds are
Hard to Germinate

Presoaking Seeds

Some people recommend soaking the seeds in water prior to germinating. This allows the seed coat to become saturated with water to break open. Because we have such successful rates of germination in hydroponics, presoaking is not recommended except for seeds that actually require this before they will germinate.


Some seeds have an extra strong seed coat that inhibits germination. This is common in larger seeds of plant fruits that expect to be eaten by an animal or bird to disperse their seeds.

Other species such as sea beans expect to be pounded along a sea surface. To mimic the natural processes, these type of seeds can be damaged in some way to break the strong seed coat.  This is called scarification.

As strange as it may seem, seeds are filed with a metal file, rubbed with sandpaper, nicked with a knife, or cracked with a hammer to weaken the seed coat. These rather brutal forms of seed abuse are actually necessary to get the seed to germinate. Scarified seeds should be planted after the process because they do not store well.

Scarification is needed mostly by trees and shrubs as honey locust, black locust, wisteria, broom, mimosa and redbud, but it is also used for common plants such as the rose.

Some Seeds Have Inhibitors

Some seeds have natural inhibiters stored in them that delays sprouting. This is often true in seeds from temperate climates. The reason this is so is that the seeds have to stay dormant through a winter and then sprout in the spring.

Abscisic Acid

This chemical develops in the seed through its creation and then keeps the seed from sprouting when it falls on the ground in the fall. During the winter the chemical degrades in the seed through enzyme action so it can then sprout in the spring.

To get seeds of this type of plant to sprout early, the seeds are gathered, placed in moist soil and refrigerated for four weeks, a process called stratification. During this time the enzymes break down and the seeds can sprout. This is a process most commonly associated with temperate native plants that require a winter season.

Phenolic Compounds

Desert plants have compounds that keep the seeds from sprouting until there is sufficient moisture for growth. The inhibitors are water soluble and allow the seed to sprout in sufficient moisture. This type of seeds only require water to sprout.

Hydroponic Nutrient Choice

There are several hydroponic nutrients on the market and most can be used to germinate seeds. If you can find a nutrient which has a higher phosphorous amount compared to nitrogen it will likely stimulate better root growth. In commercial hydroponics, Haifa Chemical in Israel has a specific nutrient for germinating seeds.

An important aspect of germinating seeds in hydroponics is that the nutrient solution have all 13 nutrients required for plants. Soil based fertilizers such as Miracle Grow do not have all 13, and so the plants will not survive very long outside of soil.

There are a wide variety of plant additive products designed to aid in the propagation of plants but most are especially for cuttings. These products include root hormone products and other specialty products for cuttings. These are probably not of much help in seed germination unless the label especially mentions that use.

Possible Problems

Excessive temperature - If the seedlings are being kept in a greenhouse, then sunlight can raise the temperature of the growing media beyond 90 degrees F, the seeds will fail to germinate and even cook, or die. Check the temperature of your growing media with a thermometer or check it with your finger. If it feels hot to the touch it probably is too hot for the seedlings. The seedling operation should be moved to a shadier place or shade cloth should be placed over the seedling growers.

Lack of moisture - Seedlings are very frail when first germinated so they should be in a relatively moist environment with humidity at 60% or higher. If seeds are being germinated in a dry environment it can be helpful to place a plastic cover over the seedlings to retain moisture. It is important to make sure there is still good airflow to the young seedlings or they will be unable to breathe.

Hydroponic Featured Products

Hydroponic Featured Products

Advanced Nutrients PH Perfect Grand Master Bundles