A Simple Guide to Starting Seeds for Hydroponics


So you’re ready to get started in hydroponics and you’re about to start some seeds…

But you have no idea where to get started?​

You’re not alone — when I first started gardening, I was a soil gardener.

Starting seeds for hydroponics systems was unknown to me until I started to build deep water culture and ebb and flow systems. Once I built those, I had to learn how to start seeds hydroponically.

One of the main benefits of hydroponics is the absolute control you have over your growing environment. Knowing that, I didn’t want to germinate seeds in soil and then transplant into a my hydroponic system, adding a bunch of dirt to the system.

There had to be another way.

Here are just a few reasons why you want to start seeds in a hydroponic system as opposed to soil:

  • Much cleaner than starting seeds in soil
  • Seedlings grow faster after germination
  • Easy to transplant into a larger hydroponic system

That second reason is a cool one. As soon as your tap root pops out, a hydroponic system is going to help it grow faster than soil and prevent it from becoming rootbound.

Step 1: Get Your Materials

You don’t need much to get started. If you build your cloner yourself, the rest of the materials will cost you under $50 bucks and will last you for quite a while. If you decide to go with a store-bought cloner, it’ll bump up the cost a bit but you’ll also be getting a much higher quality product.

Seed Starting Materials List

  1. Hydroponic Cloner – You can either build your own or use something like the Clone King and starter plugs (#3 below)
  2. 2″ Net Pots
  3. Rapid Rooter Starter Plugs
  4. Seeds – find at your local nursery if possible, or buy many places online. A personal favorite of mine is RareSeeds.com
  5. Air Pump
  6. Air Stone
  7. Tubing

Step 2: Fill The Cloner With Water

Fairly simple step here. All you need to do is fill up your reservoir to just under where your net pots sit. Don’t worry about pHing your water or using reverse osmosis right now – standard tap water will be fine.

Step 3: Set Up the Air Pump

Place the air stone in the reservoir and connect the tubing. Connect the other side to the air pump and plug it in. You should see some beautiful bubbles start to come out of the air stone. These bubbles are what will keep the roots of your seeds moist and stimulate growth.

Step 4: Place Starter Plugs and Seeds

Soak each starter plug in some water and then place it in a net pot. The moisture will help the seeds germinate.

Drop 2-3 seeds in each starter plug. We use more than 1 seed because not all seeds will germinate and we want to make sure that every starter plug has a sprouted seed – otherwise we’ll have to replant!

Step 5: Maintenance

This system is very easy to maintain as your seeds sprout.

If you want, you can place a transparent cover over the top to keep in some moisture and increase the temperature of the system, but it’s not necessary.

Make sure to moisten the starter plugs with a few sprays from a spray bottle every day so your seeds have enough moisture to sprout.

When your seeds sprout, clip off all but the strongest seedling from each starter plug.

That’s it! Your seeds should sprout in 3-5 days for most plants and you’ll be ready to start growing some truly epic plants in your hydroponic system in no time!

Video Guide

If you’re more of a visual learner, I have a three part video series from my YouTube channel​ that goes into the entire setup in detail.

Part One: The Basic Setup

This is the visual version of the blog post.  Helpful if you just need to SEE to learn (like me).​

Part Two: Making Sure Seeds Germinate

This part of the series talks about some of the maintenance and troubleshooting you might run into when starting seeds, including the infamous “why do they keep falling over” problem that a lot of beginners run into.​

Part Three: pH Water and Add Nutrients

This part of the series talks about the need to pH and add nutrients to your reservoir after the seeds have germinated.  Because they feed off of their seed leaves at the start of their life, you can get away with not doing this until the seeds germinate.

By the way, I’m using the Bluelab pH Pen​ to fill all of my pH needs.  It’s awesome!

The Green Thumbs Behind This Article:

Kevin Espiritu

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24 thoughts on “A Simple Guide to Starting Seeds for Hydroponics”

  1. Hi I just germd 4 seeds straight into inch rockwall cubes so far 3 have poped up .my question is when should i spray them with rhitzonic I’ve never used it but heard its realy good do root growth .I how in nft Thank you tim

  2. Hey kevin , Thanks for sharing this info ,

    I have seen at couple of places that netpots are dipped in water for 1.2 a inch .would you suggest this ? Also , how much should be the space between the holes, if I want grow them in same system ?

  3. If you use a cloner like the clone king, do you run it continuously after adding the seeds?
    How do you keep the spray from coming out of the cloner up through the netpots?

    • The spray shouldn’t make it through the net pots if you have growing media in it. I would run it 24/7 until I transplant just to make sure that the roots / media are getting enough water + oxygen. Hope that’s helpful!

      • Thanks!
        I noticed in a later post you were recommending Jiffy Peat Pellets. Do you think now thats a better choice than the Rapid Rooter?

  4. hey, just had a question on adding the pH to water.
    I was confused on why we don’t add pH to the water at the start of the experiment instead of waiting for them to grow.

  5. Thank you Kevin for those amazing videos and chapters!
    According to the answer that you gave to eofek, once your seeds have sprouted, I just need to put the starter plugs, and the plant in it, in a larger space, right? It is how I understand it from what I read in your chapters and in the comments.

    Then, I was wondering, is it necessary to start the seeds and grow the sprouted seeds in different deep-water-culture systems. For instance, I watched your videos about how to start seeds with your DWC system, but then once they have sprouted, could I let them where they are instead of “transplanting” them to another larger hydroponic system? I don’t really see how the transition should be.

    Thank you!

    • To your first question, yup! Just need to put into a larger space.

      For your second question, you don’t have to transplant them to a different system. I recommended that because the system in my video has the net pots very close together, so the plants will be crowded if you let them ALL grow in there. Hope that helps 🙂

  6. ok, lets assume you read this 2 yrs later 😉

    I’m totally new to this, and have no idea what comes next, after seeds sprout. I clean the starter plugs off the best looking roots and replace the plugs with ceramic beads? or — can I put everything (plugs with the plants) into ceramic beads?

    thanx a lot 4 your help

    • Hey Dustin,

      For starting seeds, you can do fine with a T5, about 2 feet by 4 feet. They don’t need a TON of light at the start…but they do need enough to get to seedling/early vegetative phase. Something like this would work pretty well!

      – Kevin

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