How Do We Clean Hydroponic Clay Balls? (5 Steps with Video)

Want to clean the dirt off hydroponic clay balls? Plant debris? Molds? Mildew? Salt buildup? You name it! I know that these are all common problems that we encounter as hydroponic gardeners. Fortunately, you met me at the right time. Years of experience with these hydroponic headaches have prepared me well for what I will share with you today!

Generally, hydroponic clay balls are cleaned using 1) hot water, 2) rinsing solutions, 3) white distilled vinegar, 4) hydrogen peroxide, and 5) bleach. When selecting a cleaning method, consider its effectiveness, cost, time consumed during use, safety, environmental friendliness, availability, and hazards.

I’m aware that there are numerous methods for cleaning hydroponic clay balls. But which one is appropriate for your situation? What are the advantages and disadvantages of each method? Let me show you how to determine which method is best for you!

1. Soak in Hot Water and Rinse

Hot water, approximately 65°C, can be used to clean hydroponic clay balls. This can be accomplished by soaking for 24 hours, then rinsing them after. This method is recommended before using the clay balls in the hydroponic system.

This method is essential to take the dust off your growing medium. It will be beneficial for people who have dust allergies, but even if you do not have allergies, working with a clean, dust-free medium is still optimum.

To properly wash hydroponic clay balls using hot water, follow these steps:

  1. Prepare two containers (one with holes at the bottom; the other without holes). For this cleaning method, you have a lot of options. You can use 1) two 15-liter buckets, 2) a strainer and a basin, or 3) a tray with holes paired with a larger tray.
  2. Fill the container with no holes with hydroponic clay balls.
  3. Slowly pour the hot water into the container.
  4. Optional: Add nitric acid or hydrogen peroxide (Note: 8 tablespoons if you are using the 15-L buckets; 2 teaspoons for smaller containers like the basin; half teaspoon for trays)
  5. Cover the container and set it aside for 24 hours.
  6. The next day, pour it into the container with holes to drain the water.
Cleaning Hydroponic Clay Balls Using Hot Water
Cleaning Hydroponic Clay Balls Using Hot Water

I have summarized the pros and cons of using hot water in the table below.

Hot water is readily
Nitric acid and hydrogen
peroxide are additional input
There is a need to
soak it for 24 hours
Needs caution during the
process since it can burn your skin
Pros and Cons of Using Hot Water to Clean Hydroponic Clay Balls

2. Clean With Rinsing Solution

To clean off the white salt deposits accumulating on the surface of hydroponic clay balls, rinsing solutions available in the market will work more efficiently than plain hot water.

Hydroponic Rinsing Solutions for Salt Buildup
Hydroponic Rinsing Solutions for Salt Buildup

An example of this is the product below, which is available on Amazon. ClearexⓇ is a rinsing solution used by some gardeners who want to dissolve accumulated salts developing in their hydroponic clay balls.

  Explore  other reasons for discolored spotting in our article about hydroponic clay balls turning white.

To use ClearexⓇ for cleaning hydroponic clay balls, implement the following steps:

  1. For every gallon of water, add 2 teaspoons of the rinsing solution.
  2. Gather your hydroton and strain it through a strainer.
  3. Allow the rinsing solution and water mixture to drain into the hydroton.
  4. Pour and drain for a total of 4 to 5 cycles.
  5. Drain and rinse with water.

To help you decide, here is a summary of the pros and cons of using rinsing solutions to clean your hydroponic clay balls.

Faster to use (no need for
a 24-hour soaking)
Purchasing the rinsing solution
is an additional cost for you
Mechanism is specific
for salt deposits
Needs safety gears like gloves during
usage, since it can irritate eyes and skin,
if exposed in high concentrations
Pros and Cons of Using Rinsing Solutions to Clean Hydroponic Clay Balls

3. Rinse with White Vinegar (Organic Choice)

When cleaning hydroponic clay balls, white distilled vinegar is a good choice if one wants to be completely organic. It is made up of 5% acetic acid which can remove grime and debris. It can also kill food-borne pathogens such as Escherichia coli.

Follow the steps outlined below, to effectively clean hydroton balls using vinegar.

  1. Combine white vinegar and hot water in a 1:2 ratio.
  2. Put your hydroton in a bucket or tub.
  3. For 5 to 10 minutes, swirl the hydroton around.
  4. Drain and rinse with lukewarm water.
Cleaning Hydroponic Clay Balls Using White Vinegar
Cleaning Hydroponic Clay Balls Using White Vinegar

For you to decide, weigh the pros and cons that are displayed in the table below.

Organic and safeStrong sour smell
Available in your kitchen
Faster to use (no need for
a 24-hour soaking)
Pros and Cons of Using White Vinegar to Clean Hydroponic Clay Balls

4. Immerse in 3% Hydrogen Peroxide

Hydrogen peroxide can be used to disinfect hydroponic clay balls with pathogens and white spots. For cleaning only a few hydrotons, mix 2 to 3 teaspoons of hydrogen peroxide per gallon of water. On the other hand, for mass cleaning, 2 cups of hydrogen peroxide must be used for a 30-gallon container.

In using 3% hydrogen peroxide to disinfect hydroponic clay balls, dilution is a key step.

Follow the steps below to clean your hydroponic clay balls.

  1. Prepare two containers (one with holes at the bottom; the other without holes).
  2. Fill the container without holes with your hydroponic clay balls.
  3. Fill the same container halfway with water.
  4. For the amount of hydrogen peroxide to be mixed, use the dilution described above.
  5. Swirl the hydrogen peroxide mixture into the hydroponic clay balls.
  6. Allow this setup to soak overnight.
  7. Drain by transferring the soaked hydroponic clay balls to the container with holes.
  8. Spray the hydroponic clay balls with water using a handheld shower.
  9. Allow them to drain and dry.
Cleaning Hydroponic Clay Balls Using Hydrogen Peroxide
Cleaning Hydroponic Clay Balls Using Hydrogen Peroxide
High disinfecting capacityMore expensive than the other alternatives
such as hot water & vinegar
It can kill fungi, molds,
bacteria, and viruses
Needs soaking for 24 hours
Pros and Cons of Using Hydrogen Peroxide to Clean Hydroponic Clay Balls

5. Soak in Bleach

Bleach is a strong, widely-used disinfectant because of its capability to kill harmful microorganisms even in hydrotons. On average, soaking hydroponic clay balls in bleach entails 2 rounds of soaking (12 hours with bleach, and 24 hours with water only).

I put bleach at the end because it should be your last resort. If you have the materials listed above, I recommend using them all instead of bleach. This is due to the fact that bleach is a more powerful disinfectant.

When using bleach to clean hydroton balls, follow these procedures:

  1. Dilute it in a 1:3 solution of bleach and water.
  2. Soak the hydroponic clay balls for 12 hours in this solution.
  3. After this period, use water to rinse them.
  4. Soak for another 24 hours, but only with water this time.
  5. Rinse and dry them thoroughly.
Bleach is usually available in homesStrong disinfectant
A cheap choiceNeeds dilution
Best to use if pathogens (e.g. molds)
are observed in the hydroponic clay balls
Longer disinfection process
(2 rounds of soaking)
Pros and Cons of Using Bleach to Clean Hydroponic Clay Balls

 Discover more on the difference between disinfectants in our article about hydrogen peroxide vs bleach. 
Reusing LECA Pebbles

The cleaning method shown above is recommended for gardeners who want to reuse their hydroponic clay balls.

Why Do We Need to Clean Hydroponic Clay Balls (4 Reasons)

Hydroponic clay balls need to be clean to avoid clogging, disease transfer, salt buildup, and pathogen infestation.

1. Avoid Clogging

When dust covers the hydroponic clay balls after purchase, it is recommended to implement cleaning methods before using them in the hydroponic system.

This is because they can contaminate the nutrient water. The solid dust particles, when they clump together can further clog air or water pumps which can cause malfunction in your hydroponic system.

The most appropriate method for this case is soaking and rinsing with hot water.

2. Disease Transfer

After every growing cycle, plant debris from falling leaves is expected to be observed in the hydroponic net pot where the clay balls are.

These leaves can be sources of pathogens that can infect the next growing cycle. Thus, cleaning the hydroponic clay balls using hydrogen peroxide, white vinegar, or bleach is advised.

3. Avoid Salt Buildup

In hydroponics, salt buildup, manifested as white spots, is common. The evaporation of the hydroponic nutrient solution leaves salt deposits on the surface of the hydroponic clay balls. Rinsing solutions can be used to remove this.

4. Pathogen Infestation

When pathogenic spores are already observed in hydroponic clay balls, it is recommended to perform intensive disinfection using hydrogen peroxide or bleach.

This can be seen in the form of white powder or white strands growing on the surface of hydroponic clay balls. This could be caused by molds or mildew.

Pro Tip: When these indicators are detected, it is critical to act quickly or your plants will suffer even more. These pathogens may be transferred to plants and, in the long run, may cause plant death.


When should you clean hydroponic clay balls?

Hydroponic clay balls are recommended to be cleaned before usage and when impurities such as dirt, debris, and pathogenic signs (i.e. white powder or white strands) are observed. It is also recommended that they be disinfected after each growing cycle to prevent disease transmission to the next set of plants to be grown in the hydroponic system.

What are the effects of not cleaning hydroponic clay balls?

Pathogen infestation is very likely if hydroponic clay balls are not cleaned. This could be due to molds or bacteria found in plant debris that fall onto the hydroponic clay balls. Another possibility is that the pH will fluctuate as a result of salt buildup. Mineral salts can lower pH, which can be harmful to plants if it becomes too low.

Summary of 5 Ways to Clean Hydroponic Clay Balls

Hydroponic clay balls can be cleaned using hot water, rinsing solutions, white distilled vinegar, hydrogen peroxide, or bleach. Each of these cleaning agents is best for certain situations.

The hot water method can be performed before using the clay balls in the hydroponic system. Rinsing solutions are the best option if the problem is salt buildup. Meanwhile, if pathogens from plant debris or molds are encountered, white vinegar, hydrogen peroxide, or bleach are effective treatments.


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