hydroponics seed germination

How to Germinate Cannabis Seeds in Hydro

We have a cannabis seedling germination page which has everything you need to know about all the different germination methods, but this tutorial is different. In this hydroponic seedling tutorial I’m going to share exactly how I do my seeds from beginning to end in a DWC/bubbleponics setup!

Just follow these instructions and you’ll end up with healthy, fast-growing plants that germinate in just a few days. It’s pretty much fail proof!

Learn How to Start Seedlings So You Can Grow Hydroponic Cannabis Plants Like This!

Supplies Needed

1.) Get Cannabis Seeds

There are a few different ways to get cannabis seeds, with the most common being ordering seeds online and growing seeds you find in weed that you buy. Learn how to research and find the right strain.

Here’s a picture showing several healthy and viable cannabis seeds

2.) Germination for Hydroponics

I’ve tried a bunch of different germination methods over the years, and the technique I prefer is for hydroponics is starting with the “Paper towel method” to germinate, putting the germinated seeds into Rapid Rooters, and installing the Rapid Rooters directly into reservoir. Lots of other germination methods as well, but this has worked best for me!

Paper Towel Method

This method is hard to mess up if you follow the instructions!

  1. Place your seeds inside a folded wet paper towel, and place it between two paper plates (or regular plates) so that they don’t dry out.
  2. Check on your seeds every 12 hours but try not to disturb them. When they’ve germinated, you’ll see the seeds have cracked and there are little white roots coming out.
  3. They should germinate in 1-4 days, though some seeds can take a week or longer (especially older seeds).
  4. Keep them warm if possible. One thing you can do to get seeds to germinate a little faster is to keep them in a warm place (75-80°F). Some people use a seedling heat mat but in most cases that’s unnecessary.

These seedlings were sprouted using the paper towel method!

3.) Place Germinated Seed in a Rapid Rooter

The Rapid Rooter should be cut open lengthwise

Gently place the germinated seed inside, root down

Most seedling plugs will go back into place easily, and you’ll barely be able to tell it’s been opened 🙂

4.) Prepare Hydro System for Its New Guest

If you haven’t put your hydroponic system together yet, now is the time! Make sure your pumps are all running, and that you’ve made a reservoir with seedling-strength nutrients. You need a home to put your new plants!

Hydro Tips & Hints

  • Air bubbles – have lots and lots of bubbles in your water reservoir. That means your air pump needs to be on all the time for the full grow. The main benefit of hydro is your plant roots are getting an unlimited amount of both water and oxygen. This is achieved by dissolving a lot of air into the water via an air stone and air pump. In order to get the fast growth, you want a lot of bubbles! A highly-oxygenated tank is also far less likely to get root rot, or suffer from other unwanted organisms growing in the reservoir!
  • Hydroguard – This supplement contains a specific bacteria that was first found in rice paddies in Japan in the 40s! It’s been common in Asia for years but only in the last several years has it been available in the US from a company called Botanicare. I highly recommend, even insist, that all hydro growers get this cheap-but-effective supplement to keep plant roots healthy!
  • Add seedling level nutrients from the beginning. A lot of growers, especially soil growers, will tell you not to add any nutrients for the first few weeks of the plant’s life. That makes a lot of sense in soil, because there are lots of nutrients contained in the soil itself for your young cannabis seedling, and giving more right at the beginning can end up giving way too much for such a young plant. However, in hydro, the only nutrients your seedling gets is what’s in the water, plus what little was contained in the seed itself. Because of that, I highly recommend giving seedling-strength nutrients to your plants from when you first fill your reservoir. Seedlings grow a LOT faster with light levels of nutrients than if you only give plain, pH’ed water at first.
  • Always check the pHfrom the beginning of your plant’s life to end the of your plant’s life

5.) Install Rapid Rooter and water the seedlings until roots reach the water reservoir – Turn on light to keep seedlings warm for best results!

Make sure to always keep the Rapid Rooter moist but not soaking wet.

If you have a top-feed, place the tube near the bottom of the net pot so the water isn’t soaking the seedling’s roots. You just want water dripping out the bottom so the root can use it for oxygen and water until it’s fully established in the reservoir.

Add your Rapid Rooter(s), and fill around the edges with extra clay pellets to hold each one in place.

Since your seed has already sprouted and been in placed into the right growing position, it’ll often pop its head out within just 12-24 hours! Sometimes you see just the leaves, but occasionally you actually see the seedling push the shell above ground. I keep the grow light on even before the seedling appears. It helps keep it warm and guide it toward the light.

When this happens the shell usually falls off on its own as the seedling grows!

The Rapid Rooter in this picture is a little too wet, which makes the seedling prone to “damping off.” If you ever notice the Rapid Rooter actually looks wet or shiny, it’s too much water. Try turning the top-feed off every few hours, or hand-watering the seedling at first. Too much moisture can kill!

Don’t use a humidity dome on seedlings unless it’s very dry where you live. If you do use a dome, consider keeping a vent open and watching the humidity. A young seedling doesn’t require high humidity, and they tend to get “wet feet” and stop growing in constantly wet conditions.

Now that your seedling in in the tank, it’s time to learn how to….

6.) Take Care of Hydro Seedlings

Here are tips for taking the best care of hydroponic marijuana seedlings:

  • Leave roots alone as much as you can with young seedlings in a hydroponic setup. It takes them a little while to get all established in the tank, almost like a fish, and during that time seedlings are much more sensitive to their roots being touched or being moved around. If at all possible, try to let the seedling grow in the same place without being moved for at least a few weeks until you put them in their final home, or even just start them in their final home!
  • Avoid reservoir changes for a few weeks if you can – Going along with what I said before about leaving the roots alone, I’ve found that young seedlings often don’t respond well to reservoir changes. Instead of changing the reservoir, just top off with half-strength vegetative nutrient water until the plant is at least 3 weeks old. It won’t be using enough nutrients to mess with the ratios, and as long as you maintain the pH and use Hydroguard your young plant will be fine with being topped off.
  • Check the pH dailyto prevent nutrient deficiencies
  • Warm but not hot temperature– I recommend hydro growers aim for 75°F, and try to stay between 73-80°F.

These seedlings are a few weeks old, and the grower plans to move them all to the

This is a time-lapse video of a cannabis seedling sprouting and growing over 13 days.

Cannabis seedlings just getting their bearings – try to avoid moving or disturbing them until they are growing fast, with new leaves every day!

Big cannabis plants ready to switch to the flowering stage

I thought hydro plants liked it cold?

Just like in soil, cannabis plants in hydro tend to grow faster in relatively warm temperatures. This is a somewhat controversial statement because a lot of hydro growers prefer to keep their temperature lower in the grow space to help prevent root rot. In fact, there are some growers right now who are reading this and shaking their heads at me.

There’s good reason to believe that hydro plants would grow better with a cool reservoir. For example, the bad microorganisms that make root rot don’t survive well at lower temperatures. Additionally, water can physically hold more oxygen at lower temperatures, which seems like it would be great for faster plant growth. Because of this, lots of growers will AC their room to 60°F, and/or get a water chiller to cool their water reservoir to a similar temperature.

I do agree that if the temperature is above 80°F, your plant is a lot more likely to get root rot. However, I personally have not found that cool temperatures are adequate to prevent root rot. Even if the temperature is 60°F, you still need lots of bubbles and a “good bacteria” supplement like Hydroguard to prevent root rot in many cases.

I’ve seen several growers buy a water chiller and still get root rot. So I personally don’t believe cold temperatures are the best way to go to keep roots healthy.

The other reason I recommend to keep it warmer is because the plants just grow faster around 75°F in hydro. If your roots go from 60°F to 75°F, you’ll see the plants start growing faster in just a day or two, just like how plants in soil grow faster when it’s warm!

Just like in soil or coco, cannabis plants in hydro grow fastest when it’s a little warm, around 75°F!

Although there may be more oxygen dissolved in the water at lower temperatures, at least in my grow tent that apparently isn’t the limiting factor to growth, because plant growth speeds up at warmer temperatures.

I’ve found that if the grow space feels cool to you, it also feels cool to your plant most likely, and it may not be growing to its full potential. Some Sativa strains are particularly sensitive to the cold, though some Indica strains from cold climates will still thrive at lower temps.
Autopsy: Why Aren’t My Seeds Sprouting?

If your seeds still aren’t sprouting and growing properly, consider the following factors.

If there’s no germination at all…

  • Temperature may be too hot or cold – aim for 75-80°F
  • Too wet – seeds and seedling roots should always be moist, but should not stay wet
  • Too dry – if a root dries out the seedling can die!
  • Bad seeds – It might not be you, it could be the seeds themselves! How can I tell if seeds are viable?

If seeds sprout, but then stop growing…

  • Temperature is too hot or cold – aim for 73-78°F
  • Too wet – even though your plants are growing with root directly in water, new seedlings don’t like “wet feet”. They don’t like for it to be too wet near the seed for too long, so make sure your Rapid Rooter or growing medium nevers looks shiny or muddy, as that means there’s too much water! Young roots that stay too wet for too long start to get mushy and die. For this reason, it’s also usually recommended to avoid using a humidity dome with seedlings unless your air is dry. Although clones love humidity domes (they need water from the air because they don’t have any roots to get water), seedlings like it a little more dry or roots tend to get mushy.
  • Too dry – less common unless you live in a very dry area, but sometimes your medium dries out too fast if you’ve got a heavy-drinking, fast-growing seedling!
  • Too much light – if the seedlings get blasted with high levels of light right away, it can shock them. They may need some time to adjust to higher light levels. Simply starting your grow light a little further away that normal is usually enough.Think sunny window at first, and start ramping up after a week of healthy growth.
  • Not enough light – if seedlings are growing long and stretchy without growing new sets of leaves, it means it wants more light.
  • No light for more than a day – if the sprouted seed doesn’t get light within 24 hours after sprouting, it may die. Once seeds are sprouted, get them in a Rapid Rooter and under at least some amount of light as soon as possible!
  • Roots damaged – If somehow your roots got damaged, it can sometimes stop the seedling from growing

Unfortunately sometimes you will never know why certain seeds just don’t thrive! It’s all part of nature 🙂

How to Germinate Cannabis Seeds in Hydro We have a cannabis seedling germination page which has everything you need to know about all the different germination methods, but this tutorial is

A Basic Guide To Seed Starting For Hydroponics

The beauty of hydroponics is that it allows you to have complete control over every input that goes into your plants: be it air, water, light, or nutrients.

You may have tasted success in your first grow system, or you may be in the process of building one now. We all know the drill.

A lot of hard reading and research, and multiple trips to your local Home Depot or gardening supply store, time spent creating your system from scratch. It is all worth the effort.

But where did you get your first plants from? The chances are that you got them as seedlings or runners from the local store.

Buying pre-grown seedlings/saplings is a good option for beginners. But in the long run, learning to start with your own batch of seeds is the best option.

Today, we will examine why this is so, and also look at all the processes involved.

Why Seeds Are Better Than Seedlings From Stores

Remember what we said at the beginning, about how hydroponics gives you complete control over all the inputs? Well, seeds are also inputs, aren’t they?

They are arguably the most important input, as they decide the type of plants and the productivity of your final harvest as well. So why would you want to leave this all-important aspect in the hands of others?


First and foremost, it is a question of freedom and choice. When buying seedlings from a store, you are dependent on their catalog. They may or may not have the varieties you seek.

Easy Access

Seeds are more abundant and easier to get. In fact, some rarer heirloom plants are often available only as seeds.

Cleaner (Less Trauma Involved)

When you do the seed starting process at home, you can plan ahead and create seedlings in a soilless medium. But when you buy from a store, you cannot guarantee that.

As you may very well know by now, soil and hydroponic systems do not go together. Soil can contain contaminants. Seedlings planted in the soil will have to go thorough rinsing and cleaning.

And if you are not careful, that can damage the fragile roots of young seedlings. When you start with seeds, this complication does not arise.


This one is pretty straightforward. Buying seeds are always cheaper than buying seedlings of the same plant.

Getting seeds started takes time and effort. And you can bet that the local store or nursery will charge you extra for that. Start at home, and you can avoid this middleman.

No Cheating!

If you want to do legit hydroponics, you have to learn how to start your own seeds. It is an integral part of growing plants.

When you buy pre-grown seedlings, it almost feels like cheating. Plus, watching a plant grow from a tiny seed will give you more satisfaction than a seedling that someone else nurtured.

Tools & Components Required For Seed Starting

Seeds require the same inputs as adult plants, only, in smaller quantities. So you will need some way to deliver light, water, nutrients, and heat.

Starting Medium/Starter Plugs

Like mature plants, seeds also need a growing medium to dig their roots into and grow. A very popular option is to buy small cubes of Rockwool, coco coir, or similar growing medium.

These cubes are also called starter plugs. They are spongy cubes that can hold air and water. Each cube has a hole in which you can drop a single seed (or several, depending on the size and type of seed).

The advantage of using cubes or starter plugs is that you don’t have to uproot the seedlings once they are ready for transplantation. You can take the entire cube and place it in a larger container filled with the same material, i.e., Rockwool or coir.

There is also another option in starter plugs, called rapid rooter. This is a moist cube made from organic materials like decomposed tree bark and peat. These may contain beneficial microbes that aid in root growth and nutrient absorption.

Another option is to ditch starter plugs entirely and use a soilless medium like perlite or vermiculite. You can just fill a tray with this material, and plant seeds in them, just as you would in natural soil.


If using rockwool cubes or rapid rooter plugs, you will need multiple small net cups to hold these in. Or you can look for specially crafted trays that contain individual slots for cubes or plugs.

If buying net pots, small 2″ versions work best, as you can keep a lot of them on a small tray.

A Container/Tray

Since you will be starting a large number of seeds, (anywhere from a dozen to fifty), it is better to look for trays or boxes that can fit these individual cups. Look for containers with a depth of around four to six inches for best results.

There are more advanced options, like building a hydroponic cloner system for your seeds. This is like a miniature hydroponic system, complete with air pumps and everything for your seeds.

For a first attempt though, a simple tray-based system is all you need.

Heating Mat

This is for regions where you cannot guarantee a temperature range between 70-90 degrees Fahrenheit at all times during the germinating and starting process.

If you live in a cold area, consider buying a heating mat to be placed under your growing tray. Seeds will refuse to sprout unless the ideal temperature requirements are met.

Grow Lights

Again, these are optional components. If it is summer and you have space where the grow tray can get adequate sunlight, you can forego artificial lights entirely. A window sill is often a great place to keep your seeds.

But if sunlight access is not available, get a decently sized grow light that can keep the entire tray surface properly illuminated.

Nutrient Solution

There are several options when it comes to nutrients for seed starting. One option is to use a diluted, half-strength solution of regular hydroponic nutrients.

Or you can go for specialized starter nutrients. There are many brands available, armed with the right mix of nutrients and compounds to encourage root growth and germination.

A Ziploc Bag

This is an optional component to get your seeds to germinate. You may want to try it out to see for yourself whether it has any advantages.

Step-by-Step Instructions – Germinating

1. Prep The Growing Medium

Whether using rockwool, coco coir or rapid rooter cubes, you need to soak them in water to prepare them. Rockwool has a high pH, so you need to wash it in a mixture of vinegar and water to make it suitable for seeds.

Ensure that the cubes are thoroughly moist. For Rockwool and coir, keep them in fresh water for an hour. Rapid rooter cubes can be moistened using a combination of pure water and mild nutrient solution for a few minutes.

2. Place the seeds

There is no guarantee that every single seed you start out with will germinate. So you may want to place at least a couple of seeds in each starter cube.

As an optional step, you can place these wet cubes inside a Ziploc bag and seal them. Place the bag in a dark corner for 2-5 days to allow for germination.

Once that is done, the cubes can be placed in your grow tray. If you opt out of this Ziploc method, simply place the cubes with the seeds in the grow tray, in individual net cups.

3. Add water and nutrients

Fill the bottom of the tray with a mix of pure water and a low concentration of hydroponic nutrients or blooming mixes.

The water level should be high enough to submerge just half an inch of your starter cube and no more. Keep an eye on the water level. If it starts to go down, add more water+nutrients to the tray.

4. Provide adequate light

One of the advantages of a grow tray is its mobility. You can move them around the house if needed. If sunlight is available, you can place them on a windowsill or patio.

If not, just move them indoors and add some grow lights. As the seeds start to sprout, increase the light intensity by bringing the grow lights closer to the tray. Do not bring them closer than six inches though.

Transplanting The Seedlings

Your seedlings are ready for transplantation if their roots are poking out of the cube of growing medium. This stage can take anywhere from a couple of weeks to more than four weeks.

It all depends on the individual plant species. Continue watering your seedlings diligently until they reach this stage. If multiple seeds germinate inside a single cube, look for the healthiest one and remove the others.

Once they are ready, carefully remove the cubes from your grow tray. You should have a working hydroponics system ready by now.

Create some space in the growing medium in your “grown-up” hydroponic system. Place the entire cube with the seedling inside this space.

Gently cover the cube with more growing medium. Water the seedling from the top with a nutrient mix in the first few days. This will encourage the young roots to push into the fresh layers of growing medium for nutrients.

And that’s all there is to it! Your seedlings are ready to grow into big healthy plants in your hydroponic system now!


Learning to get your own seed starter system is not as complicated as learning to create an entire hydroponic system. All you need is some gentle care and attention.

Starting with seeds is definitely cheaper and gives you more freedom. It is also much more satisfying than buying seedlings from the store.

And the best thing is that it takes only minimal input costs and effort. There is no logical reason not to germinate your own seeds for hydroponics.

Buying pre-grown seedlings/saplings is a good option for Hydroponic beginners. But in the long run, learning to start with your own batch of seeds is the best option. We'll know why.