Bleach is an easy and affordable way to sterilize hydroponic systems.

How to Sterilize Hydroponic Substrates

by Cindy Quarters

Substrates are an essential part of many hydroponics systems. They provide support for the plants, replacing soil in this respect, though hydroponic substrate media must always be neutral and never change the pH of the water or add any nutrients to the system. Common substrates include rock wool, coconut coir, clay pellets, sand and pea gravel. In many cases, you can use the substrate for multiple plantings, but to prevent transmission of disease it must be sterilized after every harvest.

Basic Method

Remove all plants from the substrate, and remove the substrate from the system.

Dump the substrate media out of the pots and into a bucket or other container large enough to allow you to cover it completely with liquid.

Mix 4 teaspoons of bleach into each gallon of water, and pour it carefully over the substrate. Allow it to sit at least half an hour, stirring gently if necessary to ensure all the substrate comes in contact with the solution.

Drain off the liquid and rinse well, rinsing repeatedly until you don’t get any more bleach smell from the substrate.

Shortcut Method

Take all of the pots from your hydroponic system once the plants have been harvested. Carry them to a safe area outside that cannot be accessed by children or pets. Leave the substrate in the pots but remove any remaining plant material.

Mix 9 parts water with 1 part bleach, and gently stir until it is completely mixed.

Pour the bleach solution over the pots until the substrate media is drenched. Stir the contents of the pots to make sure the bleach hits all parts of the media.

Wait for the bleach solution to drain out of the pots.

Rinse the substrate well, stirring if necessary. Once all of the bleach is gone, the pots and substrate can be reused.

Items you will need

  • Bleach
  • Buckets
  • Large spoon or stir stick


  • Use plain, unscented bleach for sterilization. Scented bleach costs more and contains unnecessary chemicals.
  • If you’re using inexpensive substrate, it is often easier to discard the old substrate and start with new, sterile media.


  • Use caution when handling bleach. The fumes can be harmful; and if spilled, it can damage whatever it touches, especially furniture, clothing and carpets. Always use it in a well-ventilated area. Keep children away when using bleach and store it in a child-safe area. Make sure that children and pets can’t get to your hydroponic substrate while it’s soaking in bleach. Discard the used sterilizing solution as soon as you are done.
  • Make sure to soak the substrate for the recommended amount of time. It’s OK to leave it longer, but cutting the soaking time short may result in your substrate not being fully sterilized.
  • Rinsing is an essential step. Failure to rinse all of the bleach residue from your substrate can leave enough bleach to end up back in your hydroponic system where it may impact water quality and affect the health of your plants.

Photo Credits

  • Thinkstock/Comstock/Getty Images