Hydroponic Seed Germination – a Full Guide

Introduction to Hydroponic seed germination

Hydroponics is an ideal method for germinating seeds and an alternative way of growing plants will be to grow plants hydroponically. Hydroponics is a more hygienic and efficient process compared to soil-based growing. It also protects plants from root rot or insects. You can control the whole system as everything is automated in this growing method. Knowing how many seeds to plant is only helpful if you can properly get them through the seed germination and propagation stages. Then, that requires careful planning of the environmental conditions for each stage of the plant’s life.

A step by step guide to seed germination process in Hydroponics

Germination is the stage during which, under the right conditions, plants break out of their seed shells and become seedlings. It begins when they’re seeds and ends just before the plants develop external cotyledons. They must be removed from the germination system as soon as you see plant parts protruding from the seed.

Requirements for Hydroponic seed germination

Requirements for Hydroponic seed germination.
Requirements for Hydroponic seed germination.

For the best success with germinating seeds in hydroponics system;

Before you start germinating, you will need the following basic items;

Grow media for the seed;

A rock wool cube – Grodan rock wool is what we use for water-based hydroponic systems or aquaponics Grodan rock wool cube

A jiffy pellet or peat moss for a coco or soil system

pH down and a pH test indicator to check pH level. pH down is an acid that is beneficial to plants.

Hydroponic germination sponge is used for seed germination. It is the ideal seed germination medium as it minimizes root damage during transplanting and separation of seedlings. Each sponge is particularly cut to allow easy germination of seeds.

For best results, you should invest in the following items;

  • A propagator – tray and lid that helps to control the seed’s environment
  • A heat mat – a heat mat that has an adjustable thermostat or stays at an even 25°C
  • Containers that are capable of holding water, Germination tray with dome
  • Rooting tonic – specialized rooting solution to speed up growth and promote thicker plant roots.
  • CFL Propagation Lights – Compact florescent lamps grow lights are softer than sunlight. So you don’t fry the sprout when it emerges, and give it a controlled gentle light from a CFL lamp. 

Hydroponic seed germination do’s and don’ts

If your germination chamber reaches an extreme temperature level on either side of the spectrum, you will not get good germination rates, if any.

Do not let seeds of media dry out. Your seeds need to be warm and moist to germinate, and forgetting to do so, or letting them get too dry between watering will likely kill them.

Keeping the germination chamber at a higher humidity will help reduce the likelihood of drying out as well as watering frequency. Using a humidity dome could help the chamber produce its humidity.

The seeds and seedlings can also be too wet. In this case, the seed generally rots before it has a chance to grow. You’ll know media is too wet if it’s soggy or falling apart. It must be quite moist, but you should see no water pooling in the tray for extended amounts of time.

Few types of growing medium for Hydroponic seed germination

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Growing plants hydroponically.
Growing plants hydroponically.
Coco Peat

Coco peat growing medium is a by-product of the coco growing industry. It comes from the coir fibers and is washed and then heat-treated before it is made into coco peat products. Most you find this in the form of large bricks.

Coco peat can store and release nutrients for extended periods to plants, and it delivers fantastic oxygenation properties. Natural pH levels of coco peat are 5.0 to 6.8, so it is bordering neutral and slightly acidic. The one downside of using Coco Peat is some of the loose particles can be washed around the system. Then, this can lead to pump blockages and reservoir sludge.

Coco Coir

Coco coir growing medium comes from the same processes as coco peat, but it isn’t ground into a fine powder. It differs because it is the hair that is found on coconut husks. It is mostly used in passive hydroponic systems, but it can also come in the form of starter cubes or larger cubes for use later in your system. It comes with all of the same properties as coco peat and is an excellent growing medium all around, but it can suffer from the same downside. It is not clean, and sediment can be washed off leading to the same pump clogs and reservoir sludge buildup. Coco coir can be rinsed before use to remove any of these loose particles.


Rockwool growing medium isn’t natural and is made by the heating and spinning of specific silica-based materials into thin threads. This is the same procedure that roof insulation is made with, and should be treated with the same precautions during use.

Rockwool delivers an ideal material which when used, has almost perfect oxygen to water ratio while being pH neutral. Most often it comes in the form of cubes or plugs at around 1-inch square that are ideal for starting seeds. Rockwool grow cubes have a pH level of around 7.8 which is a little on the alkaline side.

Phases of Hydroponic seed germination

When seeds begin to germinate, they start in a dormant state, and then as they grow, reach an actively growing state.

There are 5 parts in this phase;

Seed coat – Seed coat is the hard outer shell of the seed

Plumule – these are the first shoots or stems of an embryo plant

Hypocotyl – this is the main part beneath the stalks of the seed leaves which sits directly above the root system

Radicle – this develops into the first root

Cotyledon – these are the embryonic plant leaves that develop in seed-bearing plants. There will be one or more of these first leaves that you will see from seeds germinating. These will help retain nutrients until more dominant leaves start to grow.

When the dormant state comes to an end, the Radicle will crack, and from this, then there will be an early shoot. For this to happen, the seeds require to be in warm moist conditions. It is the function of the Cotyledon to provide the seeds with its first nutrients, they would traditionally get from the soil, but in hydroponic systems, there is no chance for them to do this. Propagation is the name given to the phase where seedlings start to become stronger, and when they develop stronger plant roots and their first real leaves. This phase of growth begins as plants emerge from the seed, and ends as they develop plant roots that have taken hold inside the germination plug. When plants have developed 2 or 3 sets of real leaves, this is the stage when they can be transplanted into the system.

Invest in an appropriate hydroponics system according to plants’ needs and your budget. You can choose an active or passive hydroponics system. Active hydroponic systems use an artificial method for germination procedure while passive hydroponic systems carry out the germination process naturally. The water culture system is one reliable system where there is no need for a growing media but you can easily grow plants in water.

Preparing your Hydroponic seed for germination

  • First, get pure, clean water and soak your start cube in it for about an hour. After 1 hour take it out and remove the excess water by shaking it gently.
  • Insert 2 to 4 seeds gently into each starter cube hole. Make provision for extra in case a few starter seeds didn’t sprout, and when they do, you can select the best and strongest of them.
  • Take the starter cubes to the nursery waiting for the seed to germinate. While in the nursery, keep adding water or the half nutrient solution to the tray, and this will get the seed to start sprouting in a few days.
  • Once the seeds start sprouting, it’s time to intensify the plant light gradually and slowly move the light closer daily until it’s less than 6 inches away from the plants. Then, start feeding the sprouts adequately with the mixed nutrient solution to accelerate its growth.

Steps of Hydroponic seed germination

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Hydroponic Corn seed germination.
Hydroponic Corn seed germination.
  • Place your seeds in the freezer for 12 to 24 hours before planting out. Then, this creates an artificial “winter” so when they are planted in a warmer place there is a clear signal to germinate.
  • If you have some rooting tonic add 1 to 2ml of it to 1L of water. These products contain Bloom Roots, Rhizotonic, or Roots Excelurator which speeds up the plant growth after the seed opens.
  • Without a rooting tonic, balance the pH level of your water down to 5.5 and tools for propagating seeds and taking clones.
  • Soak the rock wool cube or jiffy pellet in the solution for a minute to ensure the water is dispersed throughout.
  • Take the rock wool cube up out of the water and give it a slight squeeze so it is damp but not waterlogged. Then, the remaining solution can be used for watering later.
  • Plant seed at a depth of the width of the seed into the rock wool cube, and if the seed is 2mm width plant the seed 2mm below the surface. Make sure the seed is in contact with the rock wool.
  • Put the rock wool on a lattice tray inside a propagation unit. Ensure the excess water can drain from the rock wool; it is not sitting in solution.
  • Use a heat mat under the propagator to keep the rock wool at 25°C. Check the rock wool cube after a couple of days and it should still be moist, if not spray or drop some of the root solutions onto the cube. The rock wool must be kept moist but not waterlogged. With too much water there is not enough oxygen for the roots to grow and the seed and the plant roots will rot.
  • When the seed has germinated and a leaf emerged give the sprout some light. PS1 Purple lights or other CFL grow lights for 18-24 hours a day are a good way of ensuring you don’t roast the seeds in direct sunlight.
  • When roots emerge from the rock wool cube, add a solution of nutrient no higher than EC 1.0 to the tray. You can use about 1/4 nutrient strength as a guide if you do not have an EC meter.
  • Finally, when roots have emerged from the base of the cube or there are 2 to 3 nodes on the seedling, plant it out into your grow media.

Rockwool cubes for Hydroponic seed germination

Rockwool is a mainstay growing media for commercial hydroponics growers, mainly those who implement drip irrigation systems. It retains moisture well, it retains oxygen well, it never impedes root growth, it is chemically inert, and then it comes in a variety of sizes and shapes. These all benefits contribute to its popularity amongst growers, accommodating almost any plant they are growing.

Rockwool cubes are popular with hydroponics growers, and conventional growers because of their beneficial structure. When the fibers are spun it creates a structure that is perfectly suitable to retain water while holding more oxygen than typical soil mediums. The increased water holding capacity and oxygenation within the root zone is exceptionally useful when starting seeds and rooting propagation cuttings.

Another main benefit to rock wool cubes is they are considered to be a natural product even though they are manmade. This is because they originate from basaltic rock and chalk which are natural ingredients and are considered a natural product that makes them acceptable in organic growing systems, increasing their popularity. Their inert nature means growers can quickly adjust the conditions within the root zone to meet the needs of plants. A non-existent cation exchange capacity (CEC) prevents nutrients from being changed by the growing medium and made unavailable for plant uptake. The cubes can be quickly rinsed with freshwater, leaching fertilizer salts out. Rockwool cubes come in different sizes. The smallest ones work well for starting seeds and propagating stem; the larger cubes are used by growers to grow more compact plants.

How to prepare Rockwool

Before using rock wool in a hydroponics system it’s important to prepare it for use. Unlike other pH-neutral hydroponic growing media such as Hydroton and Coco Coir, Rockwool has a naturally high pH level, typically around 8.0. During the procedure there is an abundance of lime that is deposited on the fibers; lime naturally neutralizes acidity, raising the pH level.

A pH level of 8.0 isn’t optimum for growing plants so it needs to be adjusted to a level that is better suited for growth. A higher pH level will make many plant essential nutrients unavailable for plant uptake, causing deficiency symptoms. Most plants prefer to grow in slightly acidic conditions and will benefit if the pH level of hydroponic seed starting in rock wool cubes is brought down to a more acidic level. There are many ways to prepare rock wool for use, none of which are difficult, but they can be time-consuming. Due to this, you will need to account for a couple of days to prepare rock wool before being able to use it.

The first step in preparing rock wool cubes is to soak them in acidic water to lower the pH level. The acidic water will dissolve the lime that is formed on the fibers during the manufacturing process and the pH level will drop to a better level. It is best to use distilled water because of its purity but tap water can work in a pinch if it is the only thing obtainable. Adjust the pH level slowly until it reaches the desired 5.5; the pH mustn’t drop below 5.0 since it will start to damage the rock wool fibers when it is too acidic.

Then submerge the rock wool cubes in the water and allow them to soak for up to 24 hours. When they have finished soaking, remove them from the water and then carefully add them to the hydroponics system and allow the system to run without any plants until the pH level of the system stays between 5.5 and 6.0 this means the cubes are stable and can be used.

Germinating seeds

Starting seeds can sometimes be a stressful adventure and it is a constant balance between keeping them wet enough to promote germination without having them so wet they dampen off and die. Rockwool cubes are popular for germinating seeds because of their excellent moisture retention.

Moisture is a critical factor in the seed germination process. Water enters the seed through the seed coat or tiny opening known as a micropyle. The presence of water will activate the enzymatic reactions within the seed that begin the germination process.

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