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How to Clean a Hydroponic System

By: Chris | Last Updated: January 27, 2021

One of the most important aspects of hydroponic gardening is cleanliness. Maintaining a clean hydroponic system will reduce the likelihood of disease, fungus, and bacterial growth. Plants will grow faster and stay healthier in a clean environment.

If you want to get the most out of your hydroponic system, keep it clean. Keep reading to find out my favorite way to clean a hydroponic system.

Note: These methods are not intended for cleaning aquaponic systems, as they don’t take into account the ecosystem that needs to be maintained for aquatic life.

Sanitation vs Sterilization

Pop quiz time: Do you know the difference between cleaning, sanitizing, & sterilizing? I’m sure you do, but just in case let’s go through a quick rundown of what each means so we have a better idea of what we’re accomplishing.

Cleaning is basically general housekeeping around your garden. Removing dead plant matter, wiping up spills, and putting things back where they go after using them are basic cleaning steps.

Sanitizing aims to remove germs, bacteria, and fungi from surfaces with the help of a sanitizing cleaner. Notice the word remove, sanitizing doesn’t kill. If you’re sanitizing with a dirty rag, you’re basically just moving germs around on a surface.

Sterilization is performed to kill germs, bacteria, and fungi. If you use beneficial bacteria in your hydroponic system, it’s important to understand that sterilization will kill both good and bad bacteria. I still opt for full-on sterilization inside my hydroponic systems. Hydrogen peroxide is a really good sterilizer that attacks the cellular structure of nasty stuff.

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Cleaning Solutions

To tackle general cleaning and sanitation an all-purpose cleaner like Simple Green works great. Mean Green is another all-purpose cleaner that works well. You can find it at most discount stores like Dollar General for way cheaper than you’ll find it online.

Chlorine bleach is a very effective sterilizer for hydroponic components, but I’m not a fan of it. Why? Even when diluted, bleach can easily ruin clothes, burn skin and eyes, put off nasty fumes, corrode metals and other surfaces, and kill any plants or grass that it comes into contact with. If you’re comfortable using it, check out this pdf to safely dilute bleach for sanitation and sterilization.

Instead, hydrogen peroxide is my hydroponic system sterilizer of choice. Using a concentrated peroxide (28-35%) diluted down to 3% works really well. Why use concentrated? Because concentrated H2O2 uses fewer stabilizers, and results in a better oxidizing reaction in water.

Also, bulk concentrated peroxide is cheaper in the long run. A gallon of 35% peroxide costs around $80 after shipping, and it makes almost 13 gallons of 3% peroxide. If you need to dilute concentrated peroxide, use this hydrogen peroxide dilution calculator.

When it comes to sterilizing gardening tools like scissors or snips, isopropyl alcohol is hard to beat. It’s cheap, it’s effective, and it evaporates quickly. Simply wipe down the tools, and you’re good to go.


Pre-cleaning sounds kind of dumb, but let’s think of it as the cleaning setting on an oven. You spray the cleaner in the oven, and let it heat up to break up grime. Pre-cleaning a hydroponic system works in a similar way. Only, we’re not gonna be using heat.

To pre-clean your system, remove any plant matter or other large grit and grime from the grow trays. We don’t want them clogging up pumps or tubing. Once you’ve completed that bit of housekeeping, it’s time to drain the reservoir.

Fill the reservoir with enough clean water to recirculate through your system without letting the pump run dry. Add around 100-150mL of hydrogen peroxide per gallon of water to the reservoir.

Fire up the pump, and let the system circulate for an hour. This is going to help break up any of that baked-on grossness left behind by your last growing cycle and will make the following cleaning steps easier.

Once you’re done pre-cleaning, it’s time to drain the reservoir and grow chambers and get ready for the next phase of cleaning.

Disassemble the Hydroponic System

Disassembling your hydroponic system may not be your idea of a good time, but it’s an essential part of making sure you do a thorough job of cleaning. Your future plants depend on this!

With the reservoir and grow chambers emptied, it’s time to tear the system down to make it easier to clean every last nook and cranny.

  1. Disconnect all tubing. Algae is like a clingy booger, and it loves to hang out in the walls of hydroponic tubing. You’re going to want to make sure to clean the tubing well.
  2. Remove pumps and soapstones. These need a good cleaning too. It’s also a good time to inspect your soapstones (if you’re using an aerator) in case they need to be replaced. They don’t last forever. Bummer, I know.
  3. Remove substrate. If your system uses a substrate like perlite or rockwool, it’s time to remove it. If it’s reusable, move it to a large cleaning tray. I like to use the big plastic mortar mixing trays you can buy at the big box store. They’re super cheap, and tough as nails.
  4. Open up any caps or covers that you haven’t glued down. Anywhere two surfaces meet, algae and bacteria will be right there in the mix just waiting for a chance to grow.

Once you have everything disassembled, it’s time to get the party started!

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How to Clean a Hydroponic System

Now’s a good time to pull on some rubber gloves to protect your digits, and strap on some eye protection so you don’t accidentally deep-clean your eyeballs. Diluted hydrogen peroxide isn’t incredibly dangerous, but it can irritate your skin and/or burn your eyes.

Scrubbing with a brush has a tendency to fling droplets of cleaning solution, so take precautions to make sure you’re not flinging cleaner onto growing plants, or yourself.

Note: Hydrogen peroxide kills fungi, bacteria, and algae by oxidation. This process is not instant. For best results, allow things to soak for a few minutes prior to getting your scrub on!

  1. Clean the grow area
    • With your hydroponic system out of the way, this is a perfect time to clean and sterilize the grow area. 
    • If you have reflective walls in the grow area or tent, wipe them down with a peroxide/water solution. Need to know how to mix the solution? Check the first line under step 2.
    • With everything out of the way, inspect the grow area for damage. If reflective sheeting needs to be replaced, now is a perfect time.
  2. Clean the small stuff
    • Add 100-150mL of 3% peroxide per gallon of water to a cleaning container, or your hydroponic reservoir. This is where you’ll be cleaning all the small hydroponic components.
    • Cleaning hydroponic tubing. The easiest way to clean tubing and hoses is with a bottle brush. Tie a small section of stiff wire, or metal clothes hanger to the bottle brush so you can pull the brush through the tubing. Rinse the tubing in the peroxide/water solution after each pull. Repeat until the tubing is clean.
    • Disassemble water pumps. Most pumps disassemble to varying degrees to allow for internal and filter cleaning. Check out the owner’s manual to see how far to tear your pump down. Toothbrushes work great for cleaning hard-to-reach spots inside the pump.
    • Clean fittings, caps, and covers. Brushes work well for getting rid of any build-up on these components. Scrub with the brush under the surface of the solution to reduce flinging peroxide water all over yourself.
    • Inspect soapstones/bubblers. If they don’t appear to be too clogged, go ahead and give them a good cleaning with a stiff bristle brush. If they look totally shot, it’s time to replace them
  3. Clean reusable substrates
  4. Clean the big stuff
    • Scrub down the grow chambers with the same peroxide/water solution. This works best outside unless you want to scrub in the tub.
    • Clean and rinse the hydroponic reservoir. It may take a few clean/rinse repetitions depending on difficult it is to break up the salt build-up on the bottom and sides of the reservoir. This task is a LOT easier if you clean the reservoir every time you replace the nutrient solution.
  5. Re-assemble the hydroponic system
    • Once everything has been thoroughly cleaned and rinsed, it’s time to re-assemble the system.
  6. Auxiliary systems
    • If you use fans, give them a good wipe down with a soft cloth.
    • If your fan system uses intake filters and/or bug filters, now is a good time to clean them as well. If they’re reusable, toss them in the washing machine for that “like new” effect.
    • If you use them, water filters need to be replaced regularly. Now’s a good time.
  7. Don’t forget the lights
    • While they might not be growing mold, lights do collect dust and dirt over time.
    • Wipe down light surfaces including bulbs and reflectors with a soft lint-free rag to prevent scratching. Scratching is bad.
    • Glass light covers should be wiped down with 3% vinegar, and then rinsed with distilled water to prevent spotting.
    • Power cords can be cleaned with a rag or alcohol wipes. As always, don’t get electrical outlets wet. That’s bad too.
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Keeping a Hydroponic System Clean

Adding hydrogen peroxide (diluted to 3%) to the nutrient solution can help keep the system in good health, plus it can help improve the overall health of your plants. 

I currently add 10-15mL of 3% hydrogen peroxide per gallon of water when replacing nutrient solution in the reservoir. After that, I add approximately 15mL of 3% hydrogen peroxide per gallon of water every 2 days to maintain overall system health. 

If you introduce beneficial bacteria into your hydroponic system, don’t add peroxide or it will attack the beneficial bacteria.

A Note About Sterilizing Tools

It’s worth noting that you need to keep gardening tools sterilized. 

How often? After every use.

Why? Tools like knives and scissors and snips cut into plant matter. Every time you make a cut with dirty tools you risk contaminating your plants. That’s not a fun game to play!

Sterilizing tools is quick and easy. Simply soak, or dip, them in isopropyl alcohol. Ya’ know, soak the shiny metal part that comes into contact with the plants. Use a 70-100% isopropyl alcohol for best results. This also works really well to remove sticky, gummy residue from snips.

If you use things like pipettes, it’s a good idea to suck a little alcohol up into them to keep them sterilized as well.

Metering tools, like pH & EC meters, need to be cleaned and stored per the manufacturer’s directions to prolong the life and accuracy of the tool.

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How Often to Clean a Hydroponic System

There’s a lot of debate over how often you should clean your hydroponic system. Hydroponic systems can be cleaned as frequently as weekly, but this may be a waste of time and nutrients. The frequency of cleaning depends on the size of the hydroponic system, how nutrients are managed, and the type of plants growing in the system.

The short answer is that the hydroponic reservoir, pumps, and tubing should be cleaned every time the reservoir is dumped or emptied. I mean, you’re already replacing the solution so why not go ahead and spend a few extra minutes tidying things up a bit.

If you “top off” your reservoirs, a good option is to empty and clean the reservoir once the water has been fully cycled. What does this mean? Let’s say you have an 8-gallon reservoir and the plants consume 2 gallons of water per week.

After 4 weeks you have completely replaced the water in the reservoir, and it should be dumped. In this case, it would be advisable to clean the hydroponic system every 4-5 weeks.

The entire system should be thoroughly cleaned and sterilized after each harvest. If you are growing “cut and come again” crops like lettuce and kale, clean the entire system after the growing cycle of the plants is complete. 

To be completely honest, I clean my entire system every 2 or 3 growing cycles unless I see something that needs to be addressed immediately. Once you get used to your hydroponic system you’ll know when it needs to be cleaned.


Why is cleanliness in your grow room important?

General cleanliness helps limit the spread of bacteria, fungi, and algae. Additionally, routine cleaning habits like removing dead plant material helps reduce the likelihood of mold and insect infestation.

What exactly is the difference between sanitation and sterilization?

Sanitation removes germs, bacteria, and algae from a surface or area, while sterilization actively kills germs, bacteria, and algae. Disinfectants work similarly to sterilizers, but to a slightly lesser extent.

How do you clean a grow room with bleach?

Bleach, diluted with water, is best used for non-porous surfaces like counter tops, and grow trays. Bleach leaves behind a residue, which means you’ll need to rinse whatever you sterilize with bleach multiple times or risk killing plants when you refill your system.

To disinfect:
Mix bleach with water based on the bleach strength. Strength is normally noted by sodium hypochlorite percentage.
2.75% – 1/3 cup + 1 gallon water
5.25-6.25% – 3 tablespoons + 1 gallon water
8.25% – 2 tablespoons + 1 gallon water

To sanitize:
Follow the same rules as above.
2.75% – 1 tablespoon + 1 gallon water
5.25-6.25% – 2 teaspoons + 1 gallon water

Still have questions? Contact me and I’ll do my best to help ya out!

Chris Cook started Happy Hydro Farm to share his passion for hydroponic gardening! Growing your own food is incredibly rewarding both physically and mentally. His mantra - "Take excellent care of your plants, and your plants will take excellent care of you."
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