Starting Seeds for Hydroponics: Do’s and Don’ts of Germination

Do you want to grow your own food, but you don’t know where to start? Do you want to cut down on the cost of starting plants from seedlings in the store?

If so, starting plant seeds hydroponically is an excellent way for you to do both. Hydroponics provides an easy and affordable way for anyone with little money or space.

You can start many vegetables without soil before growing into mature plants ready to harvest with hydroponic gardening. They grow healthier because their nutrition comes directly from the nutrient solution rather than being absorbed from the soil.

This blog post will explain why getting started with your own seeds is better than buying them from a store, what type of equipment you need, how to germinate them, and how to transplant them into pots.

Why are seeds better than seedlings from a store?

seeds vs seedling

Starting hydroponic plants is cheaper, and it doesn’t take up as much space because they grow into mature plants faster. 

When you start seeds hydroponically, you can choose the variety and type of plants that will grow best in your growing space rather than buy seedlings from the store. And the most important thing is starting seeds means healthy plants.

One of the main benefits of hydroponics is absolute control over your growing environment. The quality of a store-bought seedling varies substantially. Fruits and vegetable seedlings from grocery stores are usually grown in sterile, unnatural conditions where they don’t have to fight pests or diseases.

The starting phase is critical, and you need to pay attention to the dos and don’ts that will help keep your plants healthy.

What equipment do you need to start seeds for hydroponics?

When you start seeds hydroponically, ta setup must meet these basic needs: water, light, nutrients, and an environment to rest. You start seeds on a different system than real hydroponic systems.

1. Starting medium

Although there are a few types of growing mediums you can use for germinating seeds, it is worth running through them to see how they work in your indoor garden.

Coco coir

Coco coir is a hydroponic medium is a material that can retain water, so you don’t have to worry about over or under-watering. Coco coir is one of your best choices for looking for something sustainable and organic. It is very light and porous and helps prevent fungus growth, which means fewer chemicals are needed!

Rockwool Cubes 

Rock wool cubes work well with an enclosed starter system with more airflow around the roots. 

These come with pre-drilled holes and have enough space for young roots to develop before being transplanted into larger containers. They also provide excellent drainage so excess moisture doesn’t build up on top of the growing medium, leading to root rot.

rockwool cubes with holes

Starter Plugs 

Starter plugs offer less room than Rockwool cubes, but they make great material. The advantage of using starter plugs is that the starting cubes are sterile, and they do not need to be soaked in water before using them. When starting seeds hydroponically, make sure you use starter plugs with a pH of around neutral (pH=around) or above.

Starter plugs without nutrients will have a higher pH range than those with fertilizers since plants absorb more from their environment when starting out as a seedling. They also dry faster, suitable for storing your starters on-hand for immediate planting needs!

2. Netcups

netcups for starting seeds

Net cups are also used by many people. Using net cups when starting seeds hydroponically, they come sterile. They do not need to be soaked in water before starting. Net cups come with a label for easy planting depth, which is helpful when starting seeds hydroponically.

3. A container/railway

Since you can start an immense number of seeds, it is better to look for trays and boxes to fit these individual cups and hold water. Look for containers whose depth is between 4 and 6 inches for the best results!

4. Humidity Dome 

humidity dome for plants

A humidity dome is essential to starting seeds hydroponically. The humidifier should be placed on a level surface at least 12 inches away from the tray and must have sufficient airflow.

Look for a humidity dome with at least two vents on each side for the best results. This will allow air to circulate and keep your starting seeds hydroponically happy!

Domes should also have enough space between them not to touch or overlap; otherwise, starting seedlings may be damaged due to lack of airflow.

5. Heating Mat

Heating mats provide warmth and moisture during the germination process, ensuring good, healthy young seedlings start! Heating mats will help offset the cold temperature from your air conditioner in the wintertime while providing a warm environment for plants on top!

6. Grow Lights

Grow lights provide the perfect conditions for helping seeds sprout indoors. They have a wide variety of different types:

  • HID Grow Lights (high-intensity discharge) is a grow light with great spectrum ranges. An HID is recommended if you plan to germinate plants in the vegetative state (i.e., growing without flowering) because it provides better spectrum ranges than other starting hardware.
  • LED lighting, energy-efficient light with lower heat output than other grow light technologies. LEDs may be preferable if you want to flower your starting plant.
  • Fluorescent lighting, inexpensive but not as effective as either HID or LEDs because it doesn’t emit enough light in the blue range of the light spectrum
  • CFLs (compact fluorescent), cheap light-emitting lots of red and green wavelengths, suitable for seed starting – no need for additional supplements!

7. Chemicals for raising or lowering pH levels

Adjusting your PH is the only way to control your nutrient balance. When starting seeds in an environment with high pH levels, adding an acid such as phosphoric or nitric acid (in tiny amounts) may be necessary to balance the PH.

Adding too many chemicals will cause a buildup of salts, so it is essential to use only what you need and not over-apply your solution.

Germinating Seeds Using Rockwool

Now let’s start that seed!

Here are step-by-step instructions to starting seeds for hydroponics:

Step 1: Prepare the seed starting medium:

There are several key points for finding a container for seed starting.

First is the size of the container. This needs to be sufficiently big enough to hold soaked cubes to accommodate future plant growth.

It can be challenging for seeds to release their baby plant growth when they’re constantly flooded with excess water. The seed needs to be at a height where the water can wick up the cube to the seed while allowing air circulation from above.

To start hydroponic seeds early on, you can use filtered water from the tap or pure water. Once you have your water in the container for germination, it is essential that you test to make sure the pH levels are within a specific range. A few growers recommend adding a half-strength solution or lower nutrient solutions to seeds at this stage. Still, if they haven’t been hydroponically grown before (if they were just watered from a glass), it’s a good idea just to add plain water.

Test the pH of your water using a pH level test and drop it to 5.5 – 6 with a liquid solution. If it’s higher than this, never go below 5.5 as this can damage the Rockwool.

Place the starter cube in the water-filled container, and let it soak for an hour to absorb. Cubes are great for hydroponic planting because they maintain the perfect balance of moisture and air. But, if you squeeze them too much, they will deform. The cubes can stay wet for a few days without adding water, so just be careful.

Do not discard the water if you are presoaking your cubes in pH-balanced water before moving them to another tray. Instead, please keep it in a sealed bucket.

Step 2: Planting Seeds into the Cubes

You can either buy cubes that come with holes in them and use those or make a hole in the top of your cube to depths up to but not more than ¼ inch deep.

Now all you have to do is take a couple of seeds and gently place them in the hole. They won’t fall, so use your finger or something that doesn’t apply pressure to push them down into the hole snugly. Once done, you can press another little piece of Rockwool on top and over the seed to cover it up.

The first thing you should do is cover the container. This can be done with an upturned tray of the same size or something that can sit across the tray without pushing on the cubes. It will create a dark environment that’s vital for successful hydroponic germination.

The container where you will be seeded starting should have an area temperature of 68 degrees Fahrenheit. If growing conditions in the nursery are below this, a heating mat can help keep your trays warm.

Step 3: Check water levels

It is best to check the water level every day once you have started growing your seeds in Rockwool. Seeds planted in that medium do not require any watering during the hydroponic germination period. Use the reserved water from step one just to keep them moist as their level drops.

It is advised not to add any nutrients at this stage because sprouts are becoming stronger and only need them once they are in your hydroponic system.

When beginning to germinate seeds hydroponically, there is a high chance of having more than one seed grow in an individual hole. As tempting as it may seem, please resist the urge to replant only a few, as pulling out seedlings’ roots can also cause damage to the other sprouts and their root growth.

After 3-4 days, the first true leaves will emerge. When this happens, carefully select the smaller of the two growing shoots, and cut off the smaller one shoot right above the cube.

Step 4: Sun / Light Exposure

It is vital to have a functioning light source for the plants when planting seeds. Planting in an area with sunlight will help seeds sprout without much trouble because they receive this input from their natural environment. However, you will occasionally rotate the trays to not lean toward the light when using a window.

Three hours per day should be enough when utilizing sunlight and five with artificial lighting sources like fluorescent bulbs. Once your seedlings get bigger, they may need up to 15 hours of light per day. This is where using a window’s major drawback is the lack of natural light. Without enough sunlight, the plants can fall over or grow too weak to stay standing, which is worsened if not caught early on.

Overhead grow lights solve this problem by giving a full quota of natural light for 15 hours per day. Because they are overhead, the plant will never lean sideways. Additionally, these plants will grow stronger and more healthy thanks to their full access to light.

One thing to note is that a seedling will also need some time in the dark, so you should have enough darkness for them when they’ve had their quota.

One last (big) caution is to make sure any grow lights are positioned far enough away from the top of the seedlings to not scorch them (depending on the light type). As they’re growing, you’ll need to raise your grow lights. Water usage might increase a little bit as the plants get bigger and healthier and if there’s heat coming off your lighting fixtures.

Step 5: Transplanting

Seeds germinate between 2-3 weeks until they can be planted into your hydroponic system. To avoid waiting, you may check at the bottom of Rockwool starter cubes and transplant when the plants develop roots that begin to protrude through the bottom. This is a good sign because plants can become root bound in their already moist cubes if left too long.

You can clear a space in your hydroponic system for your seedlings by transferring the Rockwool cube along with the whole plant to your growing media. Cover them lightly, and do top watering for a few days.

This might seem like a simple task, but plants are vulnerable to transplant shock at this stage. Not only because of the pressures of being removed from the grow tray but also transitioning into a new environment. The initial shock will take some time for them to recover from.

When transplanting your sprouting seeds for hydroponics, do it at the right time. You’ll want to get them into a hydroponic system and off of their original heat-sensitive grow cubes when they have shrunken back a bit and are ready for watering.

Why Haven’t all My Seedlings Survived?

There are numerous reasons why not all seedlings will survive, and not all can be explained. But, depending on plants, there are temperature differences that must be accounted for. If you have cool and warm weather plants as seedlings in the same environment, this could be too much of a temperature swing for either type of plant.

Other things you need to be wary of are as follows:

  • Set up everything you need for planting before taking out seeds or plantings from cold storage
  • Media drying out – seeds germinate when placed in a warm moist environment. If they dry out between watering, this can kill them or prevent them from sprouting.
  • Keeping the humidity high is essential. A humidifier or just an upturned tray on top of your grow tray will help maintain the water and dampness. A transparent dome while under lighting can be beneficial too.
  • Don’t overwater, or let your Rockwool cubes become too wet as this can lead to seeds rotting before they have a chance to germinate properly. As soon as seeds germinate, you can spray inside your grow tray rather than pouring water.
  • Don’t overfeed – when you start feeding with nutrients, this should only be when you see the first sets of true leaves. The EC of your water should be at a maximum of 0.8 – 1.2. During the early stages of life, plants will obtain all their nutrients from the cotyledons. Only when these first true leaves show they become dependent on external sources of nutrients or fertilizers.
  • Proper feeding – It is important to feed only when you see the first set of true leaves or until a final EC of the water between 0.8 and 1.2.


Starting seeds hydroponically is an excellent way for anyone, even beginners, to start out with little money or space to grow their own food and save some cash in the process!

In this blog post, we have shown you all the steps necessary to start your own plants hydroponically. If you’re still not convinced that this gardening method is suitable for you, check out our article on how to get started with seedlings at home.

Share the knowledge by posting on social media or sending a link in an email. 

Happy Planting!

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