3 Reasons Why Your Hydroton are Turning White (+ Solutions)

White spots growing in your hydroton, also known as clay pebbles, may be concerning to some. Trust me, I’ve been there. I had no idea what the effects were or what to do at first. But it is through those experiences that I have gained the knowledge and hacks that I am about to share with you today.

Generally, hydroton turns white due to 1) salt deposits from nutrients, 2) salt buildup caused by using tap, soft, and hard water, and 3) molds and mildew. This can be addressed by lowering the water level, using filtered water, providing ventilation, and misting hydroton with hydrogen peroxide, worm cast, or potassium bicarbonate.

Can you still use your hydroton once they are covered in white spots? Is it possible to clean them? Is it necessary to use disinfectants? Read on to find out!

1. Salt Deposits From Nutrients

Hydroton white spots are mainly caused by efflorescence, which is the appearance of a powdery substance on masonry products such as bricks because of evaporation of water, leaving soluble salts on the surface.

Efflorescence may appear to be a big word. But, in layman’s terms, it is simply the appearance of a white substance in a masonry product caused by the evaporation of water containing soluble salts.

If you can’t still imagine it, let us zoom into the hydroponic world.

First off, let me highlight important terms from the definition above: 1) white substance, 2) masonry product, 3) evaporation, 4) water, and 5) soluble salts.

At this point, let us simplify the hydroponics terms above .

  1. white substance = white spots
  2. masonry product = hydroton or clay pebbles
  3. evaporation = happens in hydroponics when there is high surrounding temperature
  4. water = medium in hydroponics
  5. soluble salts = nutrient (liquid or dry) mixed in water

Because we feed our hydroponic water with dissolved nutrients, and also because the hydroponic solution is in direct contact with the hydroton, the salts in the nutrients tend to be left behind when the water evaporates. These can appear on the surface as patches of white powder.


To counter this, you should lower your water level. Some gardeners recommend adjusting 2 to 4 inches away from the top surface of your hydroton.

Avoiding White Spots From Salt Deposits
Avoiding White Spots From Salt Deposits

2. Salt Buildup From Tap, Soft, or Hard Water

Using tap, soft, and hard water is not advised because they contain traces of salts (e.g. fluoride and chloride) and minerals (e.g. calcium and magnesium). These compounds have high tendencies of building up and can also lead to hydroton turning white.

Aside from salt deposits from the hydroponic nutrient water, salts and minerals can also be from the water itself.

But first let us define each of the water types mentioned in this section:

  • Tap water. This is the water type available readily. Since it does not undergo a filtration process, there are traces of minerals like magnesium, calcium, copper, and sodium.
  • Hard water. This water type has high concentrations of minerals such as calcium and magnesium that may react and become salts.
  • Soft water. This water type has lower concentrations of calcium and magnesium, but higher sodium or salt content.
   To know more about this, explore our article about water types.  

If you use tap, soft or hard water as the base of your hydroponic solution, there is a higher tendency of white spots in your hydroton.


It is recommended to use filtered water. This is because the filtration process removes these salts and minerals from your water.

Role of Temperature in the Development of Hydroton White Spots

You may have noticed that the physical process involved in the first two causes of white spots in hydroton is evaporation. As a result, every hydroponic grower must control both room and water temperature.

Pro Tip: I advise monitoring the temperature around the growing room by installing multiple thermometers. Water temperature can also be checked at least twice a day.

3. Molds and Mildew

White molds and mildew can also appear on hydroton, especially in deep water culture systems which are in contact with water continuously. This is a possible result of high humidity and poor air circulation in the hydroponic system.

Difference Between Molds and Mildew

Molds grow in a variety of colors, not only white. They also appear like a fuzzy wire! On the other hand, mildew grows on flat surfaces and may appear like powder.

Solution 1: Provide Proper Ventilation

This precaution will improve airflow and dry out the hydroton surface, preventing a favorable environment for mold growth.

   Minimizing White Spots Due to Mildew
Minimizing White Spots Due to Mildew

Solution 2: Mist Food-Grade Hydrogen Peroxide

If you observe hair-like structures, then more probably that is mold or mildew. When this happens, you can dilute food-grade hydrogen peroxide with a 3:1 ratio of water and hydrogen peroxide, respectively.

Mist this solution only on the surface of the hydroton. At this point, it is not required to soak the clay pebbles in hydrogen peroxide solution.

Solution 3: Mist Worm Tea or Potassium Bicarbonate

If you are upholding organic gardening, you can use worm/vermicompost tea. This is proven to reduce pathogen attacks, thus a beneficial spray for your hydroton and even for your hydroponic plants!

But if you are up to using chemicals, simply combine half a teaspoon of liquid soap and a gallon of water, then add a tablespoon of potassium bicarbonate. Afterward, spray the solution on the affected clay pebbles.

If the whitening returns, simply mist again.

How to Clean Hydroton (5 Ways)

To clean hydroton, one can use hot water, products like rinsing solutions, white vinegar, hydrogen peroxide, and bleach.

1. Rinse and Soak with Hot Water

  1. Prepare 2 15L-buckets (one with holes at the bottom; the other without holes).
  2. Pour the hydroton inside the bucket with no holes.
  3. Slowly fill the bucket with hot water (approximately 65ºC).
  4. Add 8 teaspoons of nitric acid or hydrogen peroxide.
  5. Cover the bucket for 24 hours.
  6. Drain by pouring it into the bucket with holes.

2. Clean With Rinsing Solution

ClearexⓇ is a rinsing solution used to dissolve accumulated salts and is available on Amazon.

To use this, one could perform the following steps:

  1. Mix 2 teaspoons of the rinsing solution to every gallon of water.
  2. Get your hydroton and place them in a strainer. (A bucket with holes below will also do.)
  3. Let the rinsing solution and water mixture flow to the hydroton. You can pour and drain repeatedly for 4 to 5 cycles.
  4. Rinse with water and drain.

3. Rinse with White Vinegar

If you want to be fully organic, white vinegar is a good choice. Follow the steps below.

  1. Mix a 1:2 ratio of white vinegar and hot water.
  2. Place your hydroton in a tub or bucket.
  3. Swirl the hydroton around for 5 to 10 minutes.
  4. Rinse with lukewarm water and drain.

4. Soak in 30% Hydrogen Peroxide

If you are cleaning just a few hydroton, you can mix 2 to 3 teaspoons of hydrogen peroxide per gallon of water. But for a 30-gallon container, 2 cups of hydrogen peroxide must be used.

To clean your hydroton, follow the procedure below.

  1. Use 2 buckets (one with holes at the bottom; the other without holes).
  2. Pour your hydroton into the bucket with holes.
  3. Fill the bucket with water.
  4. Use the dilution mentioned above for hydrogen peroxide.
  5. Swirl the hydroton with the hydrogen peroxide mixture.
  6. Soak this set-up overnight.
  7. Remove the bucket with the hydroton.
  8. Using a handheld shower, spray clean the hydroton.
  9. Drain and let them dry.

5. Soak in Bleach

I placed using bleach here at the end because this must be your last resort. If you have the materials above, I suggest choosing all of those over bleach. This is because bleach is a stronger disinfectant.

To use bleach:

  1. Dilute it in a 1:3 ratio of bleach and water, respectively.
  2. Soak the hydroton in this solution for 12 hours.
  3. Rinse them using water.
  4. Soak for another 24 hours, but this time, just use water.
  5. Rinse them and dry them.
How to Clean and Sterilize Hydroton for Reuse


Do you need to wash clay pebbles before use?

Clay pebbles must be washed before usage because the dust that comes with them may get into your hydroponic system and cause problems. Some of the potential problems are clogging and buildup.

Can I use hydroton in all hydroponic systems?

Yes, hydroton is one of the most prominent growing mediums used by hydroponic gardeners. It can be used in almost any hydroponic system—wicking, drip, ebb & flow, deep water culture, and nutrient film technique—because it is easy to work with, sterile, and lightweight.

Summary of Reasons Why Your Hydroton are Turning White

Hydroton, also known as clay pebbles, turn white due to salt deposits from nutrients, salt buildup caused by using tap, soft, and hard water, and molds and mildew.

When white spots are already dominating the hydroton, one could lower the hydroponic water level, shift to using filtered water, provide sufficient ventilation, and mist the hydroton with hydrogen peroxide, worm cast, or potassium bicarbonate.

Cleaning the hydroton can be done using hot water, rinsing solution, white vinegar, 30% hydrogen peroxide, and bleach. Furthermore, soaking periods vary from 12 to 24 hours, depending on the disinfectant.


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