Sterilizing and Disinfecting your system

Sterilizing and maintaining clean conditions inside your hydroponics/aeroponics systems is extremely important. Keeping cloning, vegetative and flowering systems clean gives your plants a fighting chance against pythium (root rot) and other harmful diseases, ensuring healthy and vigorous crops.


Cleanliness is particularly important in closed (recirculating) hydroponic/aeroponic systems due to the favorable conditions these systems present to water and airborne diseases. Failure to periodically clean a system can result in stressed plants becoming infected and rapidly spreading disease throughout the entire system. Once infected, the entire crop will experience reduced vigor and yield.

Prevention is the best ‘cure’ for disease. Sterilization between crops, adding anti-pathogen additives, and attention to system design can help combat disease.


Hot water

35% hydrogen peroxide (3% and 17% available at pharmacies, 35% at hydro stores). Oxidizes, then quickly (24 hrs) degrades to water (Sterilizing strength for 1-4 hours)

99% Isopropyl (rubbing) alcohol. Kills bacteria and viruses on contact

99% Isopropyl (rubbing) alcohol. Kills bacteria and viruses on contact

Daily/weekly system maintenance:

Dip your portable ph/tds/temp tester(s) in Isopropyl alcohol, then rinse with water before testing solutions to minimize contamination between reservoirs. When taking a reading, submerge only the sterilized portion of the tester into the reservoir.

Periodically inspect roots for signs of pythium. Consider pulling any plants with these symptoms.


Add 1.5ml 35% h2o2/gallon. H2o2 can attack beneficial bacterial; H2o2 use is not recommended when using these enzymes. H2o2 at low concentrations can add beneficial oxygen to the reservoir without killing these enzyme additives.


Mist all tools, transfer buckets, etc with isopropanol alcohol in a spray bottle, then rinse with water before use.

Weekly or bi-weekly nutrient changes are recommended. (Go longer if using enzymes to maintain).

Remove and soak all pump filters/gaskets, thermometers, strainers, air stones, etc in strong h2o2 + hot water.

Wipe away salt and slime buildup

Add Guardian Angel or other pythium-inhibiting enzymes to tank (weaker h2o2 strengths are recommended when used in conjunction with these biological additives.) Maintain enzyme strengths.

System sterilization:

Wear gloves when handling concentrated peroxide. Do not use bleach. Strong h2o2 will not ‘burn off’ slime and salt buildup by itself.

Remove all plant matter from system

Pre-flush netcups/pots with water and inspect to ensure all roots have been removed. Put netcups/pots in dishwasher, then remove and soak in strong h2o2.

If infection was present, replace any grow medium; soak gro-rocks in strong h2o2

Recommended: remove and replace all irrigation. Biologically-resistant poly tubing is can be cleaned and re-used.

Soak all ‘accessories’ in strong h2o2 (misters too, if possible)

system cleaning

Remove and sterilize reservoir by initally flushing with water and wiping with a clean cloth, then spraying 50% h2o2 with a spray bottle on all surfaces. Wait for one hour, then thouroughyl flush with water twice.

Flush system with water and do a pre-wipe (hot water + h2o2) to remove salt and slime buildup on all system surfaces.

Mix up a very strong (ie. 20%) H2o2 solution and spray it onto all system surfaces and allow to dry.

Run re-connected system with 10% h202 + hot water for several hours, dump, and flush again thoroughly with water. Don’t plant right away!

General advice:

Do not share tools and other equipment between systems or reservoirs. Isolating systems will contain any problems. Keep separate and dedicated transfer buckets, measuring cups, trays and other equipment; do not share between systems.

Keep your moms healthy and vigorous! Pythium will pass systemically to clones.

Inspect and remove unhealthy/slow growing plants early.

Use a pond strainer to keep leaves and debris out of tank

Tap water often contains elevated levels of chlorine to inhibit bacteria

System design considerations:

Isolate systems with separate tanks, irrigation and pumps.

Use reflective surfaces (mylar, white poly or titanium paint) to keep the root zone cool between misting periods.

Keep system light-tight. Cover tank (but do not seal).

If possible, use low-cost UV / biologically resistant poly irrigation hose to minimize residue buildup. Pvc plumbing is difficult to inspect and clean.

Maintain nutrient temperatures in the 65-70F range for optimum growth and o2 saturation.

Maximize o2 levels in your system: waterfall-drop your nutrient return, use airstones/venturis/skimmers

Frequently circulate nutrient solution to avoid stagnant water

1 comment to Sterilizing and Disinfecting your system

  • I agree that regular changing of water and nutrients in Hydroponc Ebb and Flow systems is critical to proper growth and flowering.
    I was not carefull of that at first and almost ruined one whole crop of nice cannabis.
    Now I change out my resivour and nutrients every ten days.
    If you do not do this on a regular basis, the water in the buckets get all black and stinky like a sewer tank.
    I caught it in time. I drained my barell and buckets. I put fresh water in the barrell and added a good amount of 35 percent Hydrogen Peroxide and ran it through a series of cycles. I had put the net pot baskets into extra buckets while flushing and cleaning the system.
    I then drained it again and refilled with fresh RO water and nutrients.
    I also put Hydrogen Peroxide into the water barrel .
    Some of the roots had started getting greyish/black at the bottoms. I trimmed a few inches off the roots and this did not seem to hurt them.
    In a few days the roots returned to their nice white look and I ended getting a good harvest out of them. I think it could have been better had I not let the water get that bad. Changing/Flushing the water is a must from now on. Thanks, Joe

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