The Magnificent Seed Starter Guide to Better Seedlings

Seed Evolution


This guide covers the Seed Starter basics. Hydroponics, specifically indoor hydroponics allows you to grow year-round. But if you live in a multi-seasonal climate like me, you will soon realize that getting your favorite seeds can be extremely difficult. Searching out testing and trying quality seed sources takes time. Doing a little homework and sourcing a few good places online to get your seeds will serve you well.


Growing your garden from seeds will not only give you personal satisfaction, but also the knowledge of where your food came from and how it was grown.  You can also learn how to tweak each of your veggie’s germination process over time to get the best crops ever!


Choosing Seeds

Seed Starter
Seed Starter, Source

Seed availability can be difficult from certain online vendors at certain times a year due to the influx of mass purchasing from commercial growers. Local big box stores limit their selection to peak growing and seasonal time. If you wish to grow year-round you will need to find out where to get seeds for your Hydroponic garden and purchase your favorite seeds ahead of the peak season in order to get what you want.


Hard to get plants and seeds

It sure is convenient to go to the local farmers’ market and purchase a few baby plants to kick start your new garden. However, properly washing and preparing the new plants to be converted to the hydroponic growing system can be messy and time-consuming. It will also most certainly require you to introduce beneficial microorganisms to your nutrient mix to keep the bad ones that came with the soil at bay. You will also be limited in your plant selection.  Some variations and air loom plants you can only get in seed form.


Seed Cost

Unless you’re purchasing some rare air loom seeds, it’s always cheaper than buy seeds instead of seedlings or a baby plant. Once you figure out how to grow out your plants and harvest your own seeds then it will become much more cost-effective and sustainable to manage your home garden.



It is important that you use the proper hydroponic system for your plants. Growing a tomato plant in an NFT system or a series of herbs in a Bucket system may work but may not give you the desired size, taste, and growth timing that meets your expectations. Knowing ahead of time what veggies you want to grow helps.



Choose high-quality seeds for successful germination. It may be worth checking out and using Non-GMO seeds. You may not be able to grow monster-sized veggies but you will have peace of mind knowing it’s natural and not genetically modified.

Various seeds, Shutterstock
Seeds, Source




Medium or Seed Starter Plugs

Coco Coir

High air and water holding capacity. Coco Coir Comes with a pH of about 6-6.8, so it will require a pre-soaking pH adjustment. Coir is not reusable but is biodegradable and sustainable.

Seeds in Peat Moss
Pre soaked Coco Coir Plugs, Source




Stone Wool

Most stone wool comes with a pH of around 8 so you will need to soak the cubes in a pH solution. They are not reusable, biodegradable, or sustainable.

Seedling in stone wool
Seedling in stone wool, Source




Paper Towel or Cloth Method

Use paper towels with no print. Saves time on wasting media on older seeds that may not germinate and saves time thinning seedlings from media after sprouting. The paper towel or cloth method is not reusable but is very Sustainable

Seeds on paper towel
Seeds on a paper towel, Source




Rapid  Grow Plugs

All-natural soilless grow plugs made of composted tree bark and organic materials. Great pH, Rapid grow plugs are not really reusable but are very Sustainable.

Rapid Grow plugs
Rapid Grow plugs, GrowWithoutSoil



Phenolic Foam (Floral Foam, Peat Foam)

This synthetic material is similar to the floral foam used by florists with similar properties so it compresses permanently and crumbles apart easily. Phenolic Foam holds a lot of water which can waterlog your seedling’s new roots or cause stem rot. Requires a pre-soak in a pH balancing solution to correct the higher factory pH. Most brands are difficult to reuse. Some are biodegradable and most are sustainable.

Seedlings in Phenolic Foam
Seedlings in Phenolic Foam, Source



Oasis Cubes

Oasis Cubes are an inexpensive alternative for germinating seeds. Similar to Rockwool starter cubes but doesn’t hold quite as much water. This material is similar to the floral foam used by florists. Not reusable, biodegradable, or sustainable.

Oasis Cube
Seedling in an Oasis Cube, Source



Clay Pebbles (Hydroton)

Clay pebbles are pretty rare for starting seeds. Usually, you will use another method and then plant seedlings, plugs, or cubes into clay pebbles. Wash pebbles as per manufacture instructions. Some require a good soak in a pH solution to balance the pH prior to use. Reusable but not biodegradable or sustainable.

Seedling in a Grow Plug in hydroton
Seedling in a Grow Plugin Hydroton, Source




Perlite has been used to aerate traditional soil and potting soil for years. Works better with larger seeds. Most perlite can be purchased sterile and pH neutral. Great aeration, but does not hold much water at all. Wash as per manufacture instructions. Reusable but not biodegradable or sustainable.

Seeds in perlite
Seeds in perlite, Source




Vermiculite has strong wicking qualities so you need to be careful of stem rot. Be sure you purchase the correct type for “hydroponics and gardening” vermiculite and wash as per instructions. It is reusable but not really biodegradable or sustainable.

Seeds in vermiculite
Seeds in vermiculite, Source



Peat Moss 

Peat Moss is rare for starting seed and not appropriate for all hydroponic systems, Best for Fodder or microgreens. Used in some aquaponic systems

Seedling in peat moss
Seedling in peat moss, Source



Propagation Tray

Tray sizes will depend on the size of your system. You may also want to use multiple smaller trays or the paper towel method as some seeds have longer germination times than others.

Black seed tray
Seed tray, Source



Humidity dome

Required for starting seeds in a tray. You can start with a 2-3” dome and move up to a taller 5-7” dome for fast sprouting seeds or microgreens.

Germination dome
Germination tray with dome, Source



Grow Light

The light type, selection, and height from the seedlings and timer settings will depend on the growing method of your system and the type of seeds your growing.

LED grow light
LED grow light, Source



Water and Nutrients

pH balanced filtered water is all that is required. Most hydroponic growers will use reverse osmosis filtered water until seedlings sprout. After the seedlings have sprouted some will add a low nutrient solution to aid in quick growth. Adding nutrients too soon may cause premature algae to grow on your media.

Nitrogen, Phosphorus, Potassium, Source



Heat mat (optional)

Some seeds will require a warmer temperature than the environment where you are growing them, Check the directions on your seed packet to see what is required. A heat mat with a thermostat is best; else you may need a timer in order to not roast the roots of your new seedlings and simultaneously grow some interesting bacteria growth. Bacteria love warm nutrient-rich water!

Seed tray with heat mat
Seed tray with heat mat, Source




Seed Evolution
Seed Evolution, Source

The following instructions will work for planting and germinating most seed types.


Prep medium

Soak and prep your medium before planting any seeds. Most will work with a good soak with a pH of about 5.3 for at least 30 minutes to balance it out your PH and not have it naturally rise over the growth of your pant life. Some growers will even soak it overnight. Rinse and fill with a proper balance PH solution before planting seeds. About 5.8-6 works well for most seeds. Some media, like Stone wool, holds A LOT of water so only add a very small amount of water to the tray. Less than ¼ the height of the cube.


Plant seeds

Place a few seeds in each cube. Give each seed room to grow.  Plant seeds at a depth equal to two or three times their width and it’s always better to plant seeds more shallow than too deep. Cover with vermiculite, peat, or perlite if you wish (optional). We have had great success not using anything to cover the seeds. Lettuce and some other seeds need light to germinate so you don’t need to cover them at all. It is best to use plants with similar germination times in the same tray else, you will have some sprouting right away while others may need a few more days time.


Add water

Use filtered water or better. Reverse osmosis filtered water is most commonly used in commercial and larger hobby systems. Don’t overwater! Remember, only fill the bottom of the tray, less than ¼ of the way up on your medium. Mediums that hold a lot of water can probably use even less, especially for seeds that are sensitive to root or stem rot.


Add nutrients

Only add a very low concentration of nutrient water after seeds sprout and have a good root system. Not having the tops of your nutrient water-soaked medium exposed to light will help you avoid early algae growth on the tops of your medium. Too much algae growth before the plants get a chance to grow not only robs your seedlings of valuable resources, it could also lead to other issues like stem rot or pythium.


Adjust Light

Cover the tray for a few days or place it in a dark area to germinate the seeds. Read the info on your seed packet and germinate seeds with similar germination times in the same tray or you will end up wasting a lot of seeds and medium. After the seedlings have sprouted you can introduce them into the light. Incrementally raise the light as required for the type of seedlings you planted.



Thin and transplant after roots grow out of the bottom of the medium so there is only 1 plant in each. For most mediums, you can simply slice down one side of the pretreated cube and sandwich the separated seedlings right in there. Make sure you place the seedlings in at the same height they were before thinning in order to avoid stem or root rot.

Transplant Ready Seedlings
Transplant Ready Seedlings, Source





Find a great seeds supplier and choose your seeds carefully.  Make sure you purchase ahead of the popular seasonal times. Decide what you are going to grow as well as what type of system and method you will be planting your seedlings into. Choose and prep the proper media for your seeds and system. Plant your seeds at the correct depth and give each of them some space. Cover with a humidity dome and place in a dark area or cover with a towel until germination. Add nutrients if desired after seeds sprout and Introduce the seedlings to the light and adjust as necessary for different plant types. Thin out and transplant into your new hydroponic system. Learn from your mistakes and continuously educate yourself to improve your growing skills.




Picture of Grammy


I'm Grammy to my grandkids and most of the authors here. My gardening career started when I was a child digging and planting in my neighbors garden in Florida. As a teenager I worked on one of the first organic farms and learned the many benefits of organic farming. As a young Mom I started dabbling in hydroponics and became hooked! My family and I learned from research and "Hard school of Knocks " ways to improve our crop growing techniques which I am willing to share with you.