How To Germinate Seeds For Hydroponics

by Lettuce Be | Last Updated: 06/23/2021

A hydroponic garden provides complete control over every element of your plants’ environment, be it light, air, or nutrients. You may have succeeded with your first grow system, or you may be in the process of building one now. We all know how it goes. Your system will require hard work, reading, and several trips to the home improvement store and garden center. All the effort is worth it.

Who provided you with your first plants? There’s a huge possibility that you got them as seedlings or runners from the local store. For new hydro growers, buying pre-grown seedlings/saplings is a good option. However, it’s best to start with your plant seed.

We will explore the reasons behind this today, as well as examine the processes involved.

The Benefits of Seeds Over Seedlings

seed starting for hydroponicsAs we discussed earlier, hydroponics provides you with complete control over all inputs. Don’t seeds count as inputs as well? It’s arguably the most important input, as it determines the type of plants and the productivity of your final harvest. What possible reason could there be for entrusting this vital aspect to others?


There’s nothing complicated about this one. It is always cheaper to buy seed packets than to buy seedlings of the same plant. It takes time and effort to successful seed starting. There’s a good chance you’ll have to pay an extra fee for that at the local store or nursery. Make it your goal to start at home, and you will avoid this middleman.

More Choices

Freedom and choice are at the core of this issue. Seedlings purchased from a store are dependent on their catalog. They might not have what you’re looking for. A greater variety of seeds is available. Sometimes, rare heirloom plants can only be obtained as seeds.

Worth It

Getting your seeds started is necessary for hydroponics to be effective. Plant growth involves it in some way. The feeling of cheating is almost palpable when you buy seedlings that have already been grown. It is more fulfilling to watch a seed grow from a seedling than a seedling nurtured by someone else.


Using soilless media is an option when starting seeds for planting at home. Buying from a store, however, is not guaranteed. Soil and hydroponic systems do not mix, as you may very well know. Contaminants can be found in soil. After planting in soil, the seedlings must be thoroughly rinsed and cleaned. You can damage young seedlings’ roots if you are not careful. This complication does not exist when you start with seeds.

Tools Needed For Seed Starting

A seed only requires a smaller amount of input than an adult plant. To provide light, water, reasonable amounts of nutrients, and heat, you will need a delivery system.

Growing Medium/Starter Plug

Like mature plants, seedlings also require a growing medium for their roots to grow in. Among the most popular growing media are Rockwool, coco peat products, or similar items. Alternatively, these cubes are called starter plugs. The spongy cubes contain both air and water. You can drop a seed into each hole of each cube (or more, depending on the size and type of seed you use).

Once seedlings are ready to be transplanted, you can transplant them into cubes or seedling plugs, eliminating the need for uprooting. This can be done by placing the cube in a larger container filled with the same material, i.e., Rockwool or coir.

Another option in starter plugs is the rapid rooter. There is a moist cube made from organic materials such as bark and peat decomposed from trees. Some of them may contain beneficial microbes that promote root growth and nutrient absorption. Alternatively, you can use a soilless medium such as perlite or vermiculite instead of a germination plug. Planting seeds in this material is very similar to planting them in natural soil.


Since you will be starting many seeds (between a dozen and fifty), you’ll need suitable trays or boxes to store these cups. For best results, choose containers with a depth of around four to six inches.
If you want to grow your seeds hydroponically, you can set up a cloner system. It is a mini-hydroponic system, complete with an air pump, air filtration, water reservoir, and everything you need for gardening. A tray-based system is all you need for a first attempt, though.

Net Pots

To hold Rockwool cubes or rapid rooter plugs, you will need multiple small net cups. You can also find trays with individual slots for larger cubes or plugs. It is best to buy net pots that are 2 inches deep, as they can be stored conveniently on small seed trays.

Grow Lights

As before, this is an optional component. It is possible to forego artificial lights entirely in summer if your grow tray is exposed to sunlight. It’s a good idea to keep your seeds on a window sill to get a couple of hours of light. However, if the tray surface cannot be adequately illuminated by sunlight, invest in a decently sized grow light.

Heat Mat

You need this in areas where you can’t guarantee a proper temperature between 70-90 degrees Fahrenheit during the early stages of the seed germination process. In colder climates, consider buying a heating pad to place under your growing tray. If the ideal temperature is not met, seeds will not sprout.

Nutrient Solution

When it comes to the solution of nutrients, there are several options. It is possible to use a solution of diluted, half-strength hydroponic nutrients. Alternatively, you can purchase specialized starter nutrients. Numerous brands are available, with compounds and nutrients that support root growth and a high germination rate.

Germination Guide

Prepare Your Growing Medium

Soak your Rockwool cube, coco coir, or rapid rooter cubes in water before planting. A rock wool cube needs to be washed in a vinegar-water solution or acidic water to lower its pH for a couple of seeds.
Be sure to moisten the grow cubes thoroughly. Coir and Rockwool should be soaked for an hour in fresh water, not tap water. You can moisten rapid rooter cubes by mixing clean water with a mild nutrient solution for a few minutes. Lightly shake out the excess water.

Plant The Seeds

Seeds don’t always germinate when they are planted; there is no guarantee. Hence, each starter cube should contain at least 2-3 seeds. Germination of seeds occurs best when the cubes are kept in the dark area for 2 – 5 days. A humidity dome is optional but can help maintain moist conditions, especially if you’re living in an arid area.

Afterward, you can place the cubes in a grow tray. Alternatively, place the seed cubes in individual net cups instead of using the Ziploc method.

Adding Nutrient Water

Add a mixture of pure water and a small amount of hydroponic nutrients, such as blooming mixes.
You want the water level to be enough to submerge your starter cube, but no more. Be sure to check the water level. Add more water and nutrients if it starts to go down. A few sprays from a spray bottle is enough. You should only start feeding nutrients when you see the first true leaves or seed leaves.

Adequate Light

Grow trays have the advantage of being mobile. They can be moved around the house if needed. Remove the humidity cover, and you can place them on a window sill or patio.
You can move them inside under grow lights if you haven’t started an indoor garden. Increase the intensity of the light as the seeds begin to sprout by bringing the grow lights closer to the tray. The distance between them should not exceed six inches, however.


If the healthy roots of your seedlings are poking through the cube of the grow medium, they are ready to be transplanted. You may need to wait 2-3 weeks for this stage. Each plant species has its characteristics. If your seedlings have not yet reached this stage, keep watering them diligently. Whenever multiple seeds germinate inside one cube, remove the bad seeds and select the most healthy one.

When the cubes are ready, remove them carefully from the grow tray to avoid root damage. Your hydroponics system should be ready by now. (We recommend a water culture system for your convenience.) Ensure that the growing medium in your hydroponic system is spacious enough. Put the seedling inside this space with the entire cube. Add more growing medium to the cube. A nutrient mix should be applied directly to the seedling in the first few days. Young roots will be encouraged to push into the fresh layers of growing medium for nutrients.

It’s as simple as that! Using the hydroponic system, you have set up, your seedlings will soon grow into healthy, large plants!


It is not as challenging to learn how to create a hydroponic system to create a seed starter system. A little tender care and attention will do. It is cheaper and easier to start with seeds. Buying seedlings from the store is much less satisfying than growing them yourself. Lastly, it requires a minimal amount of effort and input costs. Anyone can germinate hydroponic plants from seeds.