How to Clean Hydroton Clay Pebbles for Reuse in 10 Easy Steps

How to Clean Hydroton Clay Pebbles for Reuse in 10 Easy Steps

What are Hydroton Clay Pebbles?

Tiny pieces of clay subject to extremely high temperatures produce hydroton clay pebbles. Clay pebbles then expand, making them suitable for a hydroponic garden.

How to clean hydroton clay pebbles for reuse?

Hydroton clay pebbles are one of the most popular growth mediums for hydroponic and aquaponic gardens because they are lightweight, sterile, and easy to transplant and harvest.

Hydroton clay pebbles are available in most garden stores and garden centers. They can come at a hefty price, but the fact that they can be reuse makes them a cost-effective growth medium for your hydroponic garden.

Before putting the hydroton clay pebbles into your hydroponic garden, you will need to soak them for about 24 hours and rinse them to get rid of all the dust, dirt, and debris that may have settled in their pores.

Before finally placing them in the hydroponic garden, add some growing solution to give your plants the nutrients they need.

Can You Reuse Hydroton Clay Pebbles?

Hydroton clay pebbles are 100% reusable when clean well and kept in proper condition. Typically, hydroponic growth mediums either retain moisture or are reusable. Hydrotonic clay pebbles can retain moisture and are reusable too.

Hydroton clay pebbles look solid, hard, and smooth, so you may think they cannot retain moisture well. Giving it a close look, though, will explain how they can retain moisture well. They have tiny pores that are responsible for retaining moisture.

Why You Should Clean your Clay Pebbles

Since they are reusable, using hydroton clay pebbles as a growth medium allows you to save a lot of money. However, if you plan to reuse clay pebbles, you will need to clean them, especially when the plant you used died or is no longer growing. Your new plant will appreciate clean hydroton clay pebbles.

How can you tell when your hydroton clay pebbles need some cleaning? Check out for some debris or any build-up of salt on the clay pebbles. While hydron clay pebbles are excellent as a growth medium, they need to be properly cleaned to maximize their use.

After a quick cleaning with fresh water and allowing them to dry for 24 hours, you can reuse them repeatedly.

How to Clean Hydroton Clay Pebbles for Reuse

Hydroton clay pebbles are cleaned to get rid of dust, dirt, and debris, and phytotoxicity build-up over time. Phytotoxicity build-up can make your plants starve or get damaged by bacteria.

When you clean your clay pebbles, you are cleaning their tiny pores and flushing off all impurities so they can function correctly.

1. Preparation

The entire process of cleaning your clay pebbles will take a little over 24 hours Have an extra set of clay pebbles to replace the ones you are going to clean before you remove them from your hydroponic garden. This means you will need to have two sets of alternating clay pebbles.

2. Remove the used clay pebbles from the hydroponic garden.

Be extra careful if your plants are still active. Some clay pebbles may entangle with the roots. Remove the clay pebbles very carefully. Do not pull them out roughly or cut the roots.

When clay pebbles are entangled in the roots, this means your plants are using them. Roots that hold onto the clay pebbles are healthy, so do not forcibly remove them.

Examine the quality of the clay pebbles. Check the debris and build-up. While you can clean and reuse clay pebbles, if you need to clean them frequently, you may need to throw them away. Don’t worry; you should be able to use and reuse them for a long time, though.

3. Place the clay pebbles in a large cooking pot and submerge in hot water.

Choose a cooking pot that will be able to submerge all your clay pebbles in the water. Pour hot water on the pebbles. You can either boil water or use the hot water from the tap.

Shake the pot or move it around while you are filling it with hot water. Fill the pot with hot water until all clay pebbles are fully submerged.

4. Mix the clay pebbles.

Mix the clay pebbles around the pot with your hands. This is done to eject as much of the dust, dirt, and debris from the pebbles as you can. Submerging the clay pebbles in water will remove some of the impurities from the pebbles’ pores, but mixing them around will remove the impurities from the outer layer.

You can also rub the sides of the clay pebbles to loosen more of the debris. Mix the pebbles around for a few minutes until they become grimy.

5. Strain the pebbles and repeat step 4.

Use a strainer to empty the pot. You will be able to see how much debris and gunk have been removed from the pebbles.

Rinse the pot and replace the pebbles. Add some fresh hot water again. Repeat step 4. Soak the clay pebbles in water for about 4 hours and rinse.

6. Place the clay pebbles in boiling water.

After rinsing, place the pebbles back onto the pot with fresh water. Boil the pebbles. The pebbles are used to being exposed to high temperatures, so they are durable enough to withstand boiling water.

While rinsing and straining have already loosened up any build-up, boiling will fully loosen all those particles. It will also sterilize the clay pebbles. Sterilizing will eliminate any bacteria build-up.

Never forget to sterilize the clay pebbles. If you do, it is similar to washing your hands without disinfecting and sanitizing. The same goes for the clay pebbles. Missing this step means you have only cleaned the pebbles but did not disinfect and sanitize them.

You will notice some cloudy red substance settling on the top of the water while the clay pebbles are boiling. Those are all the remaining impurities and residual powder coming off the hydroton clay pebbles.

This is how important this step is. Although you have already strained the clay pebbles, some tough impurities are still left on the pebbles.

Boiling washes away all the remaining impurities from the tiny pores of the pebbles. Boiling will also kill all bacteria lingering in the clay pebbles. Boil the pebbles for at least 15 minutes.

7. Strain and rinse the clay pebbles in tap water.

After thoroughly boiling the clay pebbles, strain them. Submerge the clay pebbles together with the strainer on hot tap water. Rinse again.

Swish the clay pebbles around in the strainer and this time over running water. Once the water is cool to the touch. Use your hands to move the clay pebbles around. Give the clay pebbles a good rinse.

8. Rinse well and add pH-corrected water.

Adding pH-corrected water will ensure that all the pathogens and germs will be eliminated from the clay pebbles and will no longer spread. This will also extend the life span of the clay pebbles. Drain the clay pebbles.

9. Allow the clay pebbles to dry.

Allow the clay pebbles to dry on the strainer over the pot so they can still drain. The clay pebbles will completely dry in about 24 hours. The clay pebbles are an excellent growth medium because they are good at retaining moisture; thus they will not drain fast.

Shake the clay pebbles while you are allowing them to dry will help them dry faster. Shaking will make drain the clay pebbles of any remaining moisture.

10. Place the clay pebbles back on the hydroponic garden or in a storage container.

The clay pebbles are now ready for reuse. You can either replace them in the hydroponic garden or place them in a storage bag.

Do’s and Don’ts when using Clay Pebbles for Reuse.

Here are some tips on using hydroton clay pebbles in your hydroponic garden to ensure your plants maximize the use of this growing medium.


 Soak the clay pebbles for 6-24 hours before placing them in the hydroponic garden. The clay pebbles will be heavier, but it will be easier for your plants to get the water they need because the pebbles retain moisture.
 Soaking the clay pebbles will also remove any dust, dirt, or debris the pebbles may have collected while in the package.
Rinse the clay pebbles well after soaking. Just like after cleaning the clay pebbles, rinse them thoroughly before using.
Add in some nutrients to the clay pebbles after rinsing. Follow the package instructions with regards to the proportions or amount.
Avoid phytotoxicity build-up by removing the plants from the hydroponic garden and rinsing them. Clay pebbles, by nature, lack nutrients and have a neutral PH. However, they can still absorb nutrients you add to the hydroponic garden, which can result in the build-up of phytotoxicity.

Watch out for any whitish residue on the top. Rinse the plant and clay pebbles using pH-adjusted liquid. Make sure to do this process because phytotoxicity build-up can starve your plants.


Do not use clay pebbles as a soil substitute for outdoor gardens. You can mix clay pebbles and soil, but clay pebbles should not be used to replace soil outdoors.
Never allow clay pebbles to be dry. While clay pebbles are very good at retaining moisture, they will run dry over time because your plants get water from them. Hydronic clay pebbles are useless to plants when they are dry.
Do not reuse clay pebbles without cleaning (soaking, sterilizing, and rinsing).
Do not use peroxide or isopropyl alcohol when cleaning clay pebbles if you do not know the right way of using them.
Do not use an ordinary pot for your hydroponic garden unless you have a dedicated source of water. Regular pots can cause the growth of algae. It may also lead to some draining issues.

Final Thoughts

Hydronic clay pebbles are probably the most commonly used of all growth mediums for hydroponic gardens. This is so because they are very good at retaining moisture, thus ensuring that your plants will always have access to the water they need to develop and grow,

The ability of hydroponic clay pebbles to be reused also contributes to its popularity as a growing medium. Clay pebbles do not expire. They can be repeatedly cleaned and reused for long periods.

While clay pebbles do not have a pre-determined expiration date, throw them away when you can no longer clean or remove any salt build-up.

The lifespan of your clay pebbles is dictated by how often you clean them. It is vital to have a cleaning schedule. It is also crucial that you have a second set of clay pebbles to place in your hydroponic garden while cleaning the clay pebbles.

How to clean hydroton clay pebbles for reuse is one of the tasks you need to master if you have a hydroponic garden. A hydroponic garden with a regular supply of clean and fresh water and equally clean hydroton clay pebbles will allow your plants to grow healthy.

Jenni M
Tribal Writer

Edited by
Patricia Godwin

Patricia Godwin

Patricia has many years of experience as a content writer on various subjects, but her first love is gardening. She’s never met a plant she didn’t like and, consequently, she writes about every type of plant you can think of. Once an avid gardener with a herb garden, a succulent rockery, and a rose garden – to mention a few. Nowadays, she’s constantly on the move searching for interesting plants to bring to your attention; and explain to you all the details you need to grow, care and maintain these plants.

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