How to Clean Hydroponic System: A Step-by-Step Guide

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Brock Ingham
Brock Ingham

I don’t like a grubby bed with dirty linen, and I don’t expect my plants to sit in a grubby hydroponics system with dirty water. Leave it too long and at the very least you’ll need to get rid of algae, and at worst the whole thing can succumb to root disease. It doesn’t have to be tricky, however. With a bit of effort, you can get your rig in top shape in no time.

Hydroponic vegetables growing
Hydroponic vegetables growing

Why Is It Important To Keep Your Hydroponics System Clean?

Regularly cleaning your hydroponics setup prevents disease and helps improve the productivity of your system and the longevity of your plants. Clean at the end of each crop cycle, and after treating algae or disease.

“Over the course of growing a crop, infectious microbes accumulate and algae flourish on moist surfaces harboring fungus gnats and shore flies. Attention to greenhouse sanitation and disinfecting are steps that growers can between crop cycles.”

Tina Smith, Greenhouse Crops and Floriculture Program, University of Massachusetts, Amherst

How to Clean Your Hydroponics System.

Step 1: Prepare your Equipment

Before you start, organize your supplies. What you need varies based on the system you’re using. A basic Kratky setup will need much less equipment to clean than a large-scale Nutrient Film Technique rig.

At a minimum, you will need:

  • Cleaning agents;
  • Gloves;
  • Scrubbing brushes;
  • Buckets for soaking;
  • Clean clothes or rags;
  • Clean water and lots of it

The biggest decision to make is what cleaning agent to use. I’m a massive fan of domestic strength bleach for hard fixtures. It’s fantastic for commercial systems like the Aerogarden that come with their own cleaning cycle, and it’s just as good on reservoir tanks or grow trays.

You do need to dilute it. Aim for 1-part unscented bleach in 100 parts water. This works out to be about 1.3 oz of bleach per gallon of water.

You can also use food grade hydrogen peroxide. It’s another great choice – it produces hazardous fumes the way bleach does, but is just as effective. The best dilution ratio to use is 1 part 35% hydrogen peroxidewith 11 parts distilled water. This gives you a 3% solution that is ideal for all parts of your system.

Safety first! Always wear good quality rubber gloves and eye protection when using strong cleaning agents. Ensure you work in a well ventilated area too.

Step 2: Clear the System

Round up and discard any debris, and if there’s live plants left in the system carefully remove and set safely aside. Expired medium can be emptied from baskets or buckets and tossed.

Empty out reservoirs at this point. It can be messy business and is best done before you get moving on your grow room.

Step 3: Clean your Grow Room

There’s not much point in having a clean system in a grubby room! Once you’ve cleared the system, wipe down benches or tables with your cleaning solution. Be sure to remove dust or debris too. Mop floors, wipe walls, the works – you want a nice, hygienic environment for your newly clean rig.

Step 3: Empty and breakdown

Now that you have a clean space in which to work, break down your system. Unplug electrical components, remove filters and stones from tanks and get any small pieces in a bucket of cleaning agent to soak.

Step 4: Clean Small Pieces

Next, scrub clean and then rinse any small pieces and allow to air dry. Don’t forget air stones and the like!

Hydroponic greens
Hydroponic greens

Step 5: Scrub Reservoirs or Trays

Apply your sterilizing agent to large components of your system and get to work clearing any buildups of grime or mineral salts.

This part does depend a lot on what system you use. Deep Water System tanks often develop ‘tide lines’ that require a bit of elbow grease to shift. If you have a home built Nutrient Film Technique rig, pay attention to odd nooks and crannies in your gutters for algae buildup.

Once you’ve given everything a thorough once over, rinse if needed to remove any remaining sludge.

Step 7: Sterilize the System

Put your system back together in a ‘pre-planting’ configuration and sterilize your rig.

Again your technique will depend on what system you’re using. A passive DWC setup will only really need a final wipe down with sterilizing solution. For larger active systems, fill the system with sterilizing agent and run it through pipes, trays and pumps, ensuring air stones and the like are also in place. Allow 4-6 hours of sterilization for active systems.

Step 8: Flush the System

After the sterilization cycle, empty the rig once more. Replace the contents of the reservoir with fresh water and run the system to remove any residue. I like to run it three or four times to be certain the system is clean.

Wipe down any spills from counters or benches and put away all your equipment. Discard any leftover cleaning solution – it loses effectiveness over time and must be mixed fresh each time.

Once the system is dry you will have a clean hydroponic system that’s ready to plant.

Hydrogen Peroxide


Can You Use Hydrogen Peroxide to Clean Hydroponic System?

35% food grade hydrogen peroxide is one of the best substances to use when cleaning your hydroponic system. It breaks down into oxygen and water, leaving no harmful residues behind. It’s so well suited to hydroponics that some growers use it to boost the oxygen levels in their solution, or to treat root rot without killing the crops.

Always dilute it to a 3% solution before use. That’s one part hydrogen peroxide to eleven parts distilled water.

How Often Should I Flush My Hydroponic System?

The number of times you flush will depend on what sterilizing solution you decide to use. Bleach based solution is very effective, but needs some serious flushing afterwards. Three or four cycles is best. Hydrogen peroxide has a shorter lifespan, and two or three will be sufficient.

How Do You Disinfect Water in Hydroponics?

Sometimes it’s important to disinfect your system without shutting it down. Perhaps you have long term crops that are at risk of root rot, or you’ve become over-run with algae midway through your cropping cycle.

The 3% hydrogen peroxide solution mentioned earlier can added to your nutrient solution. It’ll move through the system and kill off pathogens around the roots. Add 3ml of this diluted mix per quart of nutrient solution directly into the reserve tank, dosing every three or four days.

How to Clean Algae From Hydroponic System?

A thorough cleaning process as outlined above will remove algae from your hydro rig. It’s one of the great persistent problems of hydroponic setups, so don’t feel too bad if you’ve had a bit of green fluff develop from time to time.

Algae can be kept under control with lower temperatures, along with preventing light reaching the nutrient solution inside the rig. Maintaining a high oxygen level in your nutrient solution will also help keep it in check.

Final thoughts

I wash my plates after dinner, and my clothes after wearing them, so it only makes sense to clean my hydroponic systems one I’m done with each and every crop. Growing indoors does cut down on pest and disease risks, but good hygiene and a clean system are important to keeping your plants in their best health. No matter what type of system you use, a clean system will ensure consistently successful harvests.

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