Cleaning Hydroponic Systems

A dirty hydroponic system can harbor pests, pathogens, bacteria, and fungi. Cleaning hydroponic systems prevents a lot of issues that damage plants. Not only do you need to clean between different harvests, you also have to clean it regularly. Obviously, you cannot clean the same way when you are growing plants. Still, cleaning is paramount whether plants are in your hydroponic system or not.

How often to clean hydroponic systems?

When you have plants growing, clean your reservoir every time you do a large water change. Keep the rest of your system clean by keeping drains clear and unclogged, removing dead plant materials, and pruning old leaves. After a harvest, thoroughly sanitize and sterilize hydroponic systems. This keeps organic material from decomposing and transferring to a new crop. It also keeps any contaminants from your new plants.

Sterilizing or Sanitizing?

They sound similar, but sanitizing and sterilizing are different processes. Sterilizing hydroponic systems is more intense and should remove any microbes and bacteria from the system. Sanitizing is more like regular cleaning. When you sanitize a system, you are not getting rid of every little microbe. You are just keeping your system and grow room in good, clean order.


  • Is a regular, ongoing process
  • Includes typical maintenance
  • Includes removing dead organic material (from plants), cleaning spills, dusting
  • May include cleaning air filters
  • Includes cleaning a reservoir during large water changes


  • Means cleaning the hydroponic system and grow room
  • Usually done between crops (after a harvest, before starting new plants)
  • Eliminates all microorganisms
  • Does not happen as frequently
  • Uses different cleaning solutions than sanitizing

For healthy plants, only sanitizing, or only sterilizing, is not enough.
Both are necessary.

A clean hydroponic system prevents a lot of problems before they even start. Without regular cleaning, harmful bacteria and other microorganisms build up. It has not always visible, but the mess is there. Sanitizing your hydroponic system is part of an ongoing routine. Consider it part of your maintenance just like changing your water and feeding your plants. Sterilizing your hydroponic system is part of a routine, although it is less frequent. It is still an important process and keeps your plants from getting sick.

What to Use to Clean Your Hydroponic System

What you use depends on whether you are sterilizing or sanitizing your hydroponic system. If you are sterilizing your system and grow room, you should not have plants growing. That means you can use stronger products. When you are sanitizing a grow area, plants may still be growing. So you will have to use gentler products. Most of the tools you use are the same, whether sanitizing or sterilizing.

Products for sanitizing:

  • Vinegar and water – 50/50 mixture
  • Water and hydrogen peroxide (food grade, up to 35%)
  • Natural, food safe cleaning solutions

Products for sterilizing:

  • Bleach and water mixture
  • Chemical cleaning solutions
  • Isopropyl alcohol

Tools for either:

  • Microfiber cloths
  • Protective gear (glasses, gloves, etc.)
  • Scrubbers and sponges (brand new or thoroughly sterilized)
  • Trash bags or vacuum
  • Pruning tools
  • Scrub brushes (long and short handled)
  • Broom and dustpan
  • Mop and bucket
  • Clean clothes for wet/dry use
Cleaning Equipment

Check Our Hydroponic Cleaning Guides:

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Frequently Asked Questions

Why shouldn’t you use soap to clean your container?

Soap does a good job of cleaning ourselves, our homes, and even our pets! For plants though, they are a bit different. They do not always handle the ingredients in soap very well, and they can have trouble growing as a result. The other problem with using soap to clean your container is it can be hard to completely rinse off. Cleaning hydroponic systems also means making sure no contaminants are left. Even if you cannot see it, there can be some extra left, so try and use a mix of water and vinegar instead.

 If I am growing organically, can I use non-organic solutions to clean my hydroponic system?

There are some products you can use that are not organic. That said, the solutions cannot contaminate your plants or natural systems (so flush your system afterward). The National Organic Program specifies what ‘synthetic’ (non-organic) products are allowed. These products undergo evaluation and are considered GRAS (Generally Recognized as Safe). Some permitted products include isopropanol and ethanol, as well as other alcohols. Look at the List of Allowed and Prohibited Substances for more detailed information.

Can I clean an airstone?

Technically, yes you can. That said, all the tiny holes make it hard to get harsh chemicals out. Use something plants can tolerate, like vinegar or hydrogen peroxide. Then, connect it back to the air pump and let it run in clean water. Depending on the size of your system, and your airstone, it may just be easier to replace the airstone when you sterilize your tank.