How to clean a hydroponic system

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Keeping your hydroponic garden up and running means understanding how to maintain it. Growing our produce with a quality hydroponic system can help make your garden life easier and more exciting. But learning how to clean a hydroponic system is the base of a flourishing garden full of hydroponic vegetables like tomatoes to parsley!

A community of hydroponic companion plants cannot support one another in a poorly kept environment. Knowing how much water you need in your system isn’t enough. A clean system will help your plants grow efficiently and protect them from bacteria and algae that can stunt their growth. Here’s a quick guide to cleaning your hydroponic system to help make your cleaning journey easier.

The Ultimate grow room sanitization

Keeping your grow room is just as essential as cleaning your system to prevent any lingering bacteria or dirt from infecting your system. Your floor or walls can have droplets of reservoir solution that can easily contaminate your plants. Cleaning your grow room will also contribute to your overall hygiene in keeping a healthy environment for growing produce.

First, use isopropyl alcohol and wipe the gardening tools you used or new garden tools you plan on using. Mop the floors, scrub the walls, and clean the tables with a rag and all-purpose cleaner.

Thoroughly dry your grow room after rinsing off the soap. Do not leave any puddles of water or soap to prevent infestation; germs can travel through liquid, especially in an aqua system.

Precleaning – Knowing how to clean a hydroponic system pre-gardening

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Ensure your grow room is clean and sanitized before deciding your hydroponic is ready for the growing cycle of plants; They will take time to grow in their respective environments, so ensure you are planting on a clean slate. There are different parts of a hydroponic system to familiarize yourself with before cleaning or preparing for a well-built and prepped for your garden! 

There are different types of hydroponic systems; each has a specific technique for delivering nutrients. But all of them have common parts that make them a hydroponic systems. 

  1. Tray (Growing Chamber)

The growing chamber will help keep your plants in place while submerged in the reservoir. It also keeps the plants safe from external factors that invite bacteria like algae that can affect their growth. Trays protect plants from pest infestation, heat, and light.

Plants need specific conditions to grow; extremes, like too much or insufficient light, can result in growth stunts.

The size and shape of a tray will depend on the plants grown and the type of hydroponic system you will use. Bigger plants have larger root systems, meaning a big tray is needed to support them.

  1. Reservoir

Reservoirs carry the nutrients to the plants by having their roots dipped in water solutions to absorb the necessary nutrients to grow. The nutrient solution travels by a pump in the reservoir. It can also be a growing chamber since you can permanently dip the roots.

Reservoirs must be lightproof to prevent microorganisms, algae, and other fungal growth. Even low light can cause microorganisms to thrive, so the best move is to cover, paint, or wrap them with plastic sheet insulation.

  1. Submersible pumps

Most hydroponic systems need submersible pumps to pump the nutrient solutions down in the reservoir to the growing chamber for the plants. The minimum amount of water in your hydroponic system will help you get an idea of the size of your pump.

Also, consider how high the water is from the water line to the reservoir to the roots when pumped. The wrong measure may cause overflowing and splashing of the solution on the floor, risking contamination in other sections and plants.

  1. Delivery Tubes

Also known as the delivery system, delivery tubes spray the water solutions upwards to the plants’ roots. They reach the tray and then to the reservoir. Delivery tubes are efficient but are prone to clogging. 

You can create these with quality and affordable combinations of materials, such as using the following:

  • blue/black vinyl tubing
  • PVC tubing and connectors
  • standard garden irrigation and connectors

Stack some extras in your storage when removing the delivery tubes to clean out the clog. 

  1. Air pumps/Aerators

Aerators may be optional in a hydroponic garden, but they offer oxygen to the water solutions to help your plants breathe and grow. You can find them in stores that sell aquarium supplies!

Air pumps are placed in reservoirs to pump tiny bubbles to provide optimal amounts of oxygen to prevent your plants from suffocating, especially in soilless systems. The bubbles also help keep the water solutions circulating, ensuring it is well-mixed at all times and preventing pathogens.

  1. Grow light

Grow lights help provide the amount of light needed for your plants to perform photosynthesis. Unlike regular household lights, grow light radiates color spectrums that mimic sunlight. They help complete the required hours for each plant. However, this is unnecessary if you set up your hydroponic garden under natural sunlight.

You can purchase grow lights in markets or online stores that sell LED emitters.

Maintenance – Keeping your hydroponic system clean

Performing general cleanliness in your grow room can help prevent algae infestation and the build-up of different bacteria that can lessen the effectiveness of the nutrients you’ve curated in your hydroponic systems.

Of course, everything requires cleaning, but a clean water system is relevant to ensure your plants’ nutrients are transferred and circulated successfully.

Cleaning solutions

Cleaning agents or cleaning solutions are your allies in maintaining your hydroponic system. You will mainly need four cleaning agents: Isopropyl Alcohol, All-purpose cleaners, Hydrogen Peroxide, and Vinegar. 

Isopropyl alcohol and all-purpose cleaners are for general cleaning, while vinegar is for a full-on cleaning of your system.

  1. Using the clean rag and isopropyl alcohol, wipe and sterilize the following gardening tools:
    • scissors
    • snips/trowels 
  1. Put all-purpose cleaners in a gallon of water and soak your mop or rags to wipe down the floor and tables. 
  2. Soak the tubes and other parts in a vinegar solution.

Use hydrogen peroxide diluted to 3% to sterilize the hydroponic system since levels of 28% to 35% can damage the plants; fewer stabilizers result in a better oxidizing reaction in water. Bleach is also an option, but it may still be corrosive. 

Never mix your chemicals haphazardly, even in storage. Organize your cleaning solutions by labeling them so you won’t mix chemicals that can damage your system or plants.

Tools needed

Are you ready to clean your hydroponic system? Ensure to equip yourself with the following cleaning resources before you begin:

  • Rubber gloves
  • A face mask
  • Sponges and scrubbers
  • Bottle brushes
  • Clean, dry cloth or rags
  • Buckets
  • Small plastic bins (for soaking small pieces)
  • A water source


Once you have gathered your cleaning agents and tools, let us begin with a step-by-step guide by Flora Flex.

1. Clear the plants

Remove all plant matter or large grit and grime from the grow trays to avoid clogging the pump and the tubes. If there are some plants you won’t remove yet, trim and rinse the roots before hanging them in a jar.

2. Drain your system

Next is to drain your entire system. Empty your hydroponic tank of the solution. It is best to be thorough, so if you see a shallow layer of solution at the bottom you can take a sponge to soak the solution or use a wet-and-dry vacuum to remove it from the reservoir.

3. Disassemble your system

Take your hydroponic system apart for sterilizing. First, disconnect the tubes; you can see the algae forming from there. Follow this with your pumps and soapstones. 

4. Separate and soak smaller pieces

Mix a gallon of water with 3% diluted hydrogen peroxide in a basin or bucket. Place the smaller parts of your system such as air pumps, nozzles, and some tubes into this solution. 

5. Do an initial scrub of the Basin

Fill one of the empty buckets with the same type of solution used for the dilute hydrogen peroxide bath. Dip a scrubber or sponge into the solution and scrub the basin from top to bottom. Do not leave any nutrient or mineral residue on the walls. 

6. Perform a cleansing cycle

After the initial scrubbing, fill your reservoir with the same solution. Add more of this solution to perform a cleansing cycle. Let your system run for around 4 to 6 hours until the solution has passed through every tube, cleaning it.

7. Flush the system

What’s next is to flush that solution out. Fill the basin with clean water and let it run through your system. Repeat this around three times until you are sure there is no solution left in your hydroponic system.

8. Let it dry

Finally, your hydroponic system has been cleaned and sterilized. All you have to do now is dry all possible areas with a clean cloth or towel and let them dry completely before using them again.

Avoid leaving puddles of water inside pots or any other container; Bacteria can take hold and cause disaster for your plants. Use a fan and turn on the grow lights to speed up the drying process and avoid standing water.

Sanitization vs. Sterilization

Is there a difference? Although sanitizing, sterilizing, and cleaning is often interchanged, there is a slight difference. Both represent different stages in the cleaning process of your hydroponic system.

In preparing to clean your hydroponic system, you first have to “clean” your space, meaning observing general cleanliness. Re-organize used equipment: remove dead plant matter, and empty stagnant buckets, among other things. Cleaning makes sanitizing and sterilizing a lot easier.

While growers are likely to keep their stations tidy, it’s a different matter when systems themselves require tending to. This is when sanitizing and/or sterilizing is needed. To sanitize is to get rid of germs, bacteria, and fungi using a sanitizing cleaner. This does not necessarily kill germs but removes or wipes them away.

Wiping away spilled water, removing dead plant matter, and dust, and wiping through air intake filters are very important as these can be breeding grounds for bacteria that can quickly spread to your plants.

When that’s not enough, that is when you sterilize. Though this kills germs, bacteria, and fungi, it also kills good bacteria.

Sterilizing prevents pathogens or mildew from settling in your plants. It is best for after a harvest.


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Now that you’ve been accustomed to how to clean a hydroponic system, you may be thinking of other related questions to ensure you’re growing healthy food from a fresh water system.

How do you clean algae out of a hydroponic system?

Not everything green is good, especially in hydroponic systems. You might come across fuzzy greens around your plants and sprouts, but while they may seem harmless, these algae may suffocate their roots.

Algae are present where there is light and water; hence while you’re farming for plants, you are also farming algae. Fortunately, cleaning algae without sacrificing your plants is possible! 

1. Remove your plants

Remove your plants from the system. Trim the roots and rinse if you cannot remove the plants from their area, then suspend them over water in a jar. Do not return plants covered in algae.

2. Clean your water reservoir first

Your water reservoir is up next. Rinse it with dish soap and water first. Next, fill it with 2-3 teaspoons of food-grade hydrogen peroxide per gallon of reservoir water. Run the solution through your system for 15 to 20 minutes until the solution cleans all of the tubes. Then empty the water reservoir then rinse it again.

3. Disassemble the entire system and handwash.

Disassemble your hydroponics system, including tubes and the reservoir. Detect if there is still any algae growth. After such, you should hand wash it with dish soap and hot water. Remember to be careful with the hot water as it can warp the parts.

4. Soak the parts in vinegar. 

If you have a large sink or bucket, submerge the entire piece in a solution of 1 part vinegar to 20 parts warm water and soak as many times as you like.

5. Replace the reservoir and run the system. 

Run the watering system for 5 minutes before planting again to dilute any remaining hydrogen peroxide in the lines. Once everything is clean, you can start your backup or close it down. If you choose to close it down, let it dry out first so algae will not return immediately.

How often do you need to clean a hydroponic system?

Generally, you must always keep your system tidy, but that might be too much work! The water tank would require full-on water changes, but too often may shock and endanger your plants.

The safest choice is to change your water for 2 to 3 weeks for an average-length hydroponic system. However, smaller hydroponic containers may cause a shorter time interval. Be sure to scrub the water tank with plant-friendly solutions while doing it.


Hydroponic gardening is one of the many wonders of modern farming.

Hydroponic gardeners must take extra caution as clean water is the key to a clean system! Keeping things clean in your hydroponic systems will not just benefit your plants but also your human health to ensure you’re adding fresh ingredients into your meals every day.