Hydroponic Hygiene

By Lynette Morgan
Published: March 1, 2016 | Last updated: April 26, 2021 11:46:49
Key Takeaways

The “kill everything” approach to sterilizing a hydroponic system during a massive cleanout is an outdated idea. After all, you don’t want to kill the good microbes that your plants love. Instead, take a balanced approach when it comes to hygiene, which will help keep the bad bugs out and provide an ideal work environment for you.

A sparkling-clean, tidy indoor garden is not only nice to work in, but it also minimizes pest and pathogen problems. Keeping in mind that many of our gardening enemies have well-developed means of dispersal and survival and are often too small to see, we need to take a proactive approach to keeping them out.


This means a regular sanitation program, one that fends off pests and kills pathogen spores without contaminating our hydroponic systems with unwanted residues. Apart from preventing plant diseases, practicing good sanitation and hygiene ensures the fruits, vegetables and herbs we produce don’t become contaminated with pathogens that can cause food-borne illnesses.

Indoor gardens and well-maintained greenhouses allow for a higher degree of cleanliness and hygiene than outdoor gardens, where soil, manure, water, and exposure to birds, rodents and other animals create a higher risk of contamination.


However, an enclosed growing area is no guarantee that pests and diseases won’t take hold at some point. The higher density of plants in indoor gardens, combined with year-round cropping, can lead to a buildup of biofilm such as algae on surfaces, and pests and pathogens that breed without seasonal interruptions. Fortunately, most hydroponic systems these days are made of heavy-duty plastics that are easy to sanitize and keep clean.

Basic Steps to Good Garden Hygiene

There are some basic steps to keeping indoor gardens and greenhouses relatively clean. The first is removing plant debris from the growing area as soon as possible, including dead plant material, leaves and root systems, and used growing media. The organic matter can be composted, ideally well away from the other crops, and covered with plastic so the carry-over of insect eggs and disease spores does not occur.

In hydroponic systems, algae can be a common problem on many surfaces and should be manually removed as often as possible. Fungus gnats are highly attracted to wet conditions where algae has grown. These pests not only damage plants, but can also carry pythium and other disease pathogens. Any issues with pests that create food safety concerns, such as cockroaches, rats and mice, need to be dealt with by a professional exterminator if necessary. Floors in growing areas should be cleaned regularly—a wipe down with disinfectant or hot water and detergent is usually sufficient for concrete and other types of hard floors.


For larger areas and commercial greenhouses, other protective measures often include the use of insect mesh screens over vents and entrance ways. At a higher level, anyone entering more sophisticated growing environments may need to change into clean clothing and footwear, and wash their hands or wear gloves before handling any of the plants. On a smaller scale, as a basic precaution, washing hands before working with food plants is always advisable.

While this level of basic hygiene goes a long way towards preventing major problems, all hydroponic systems need a complete shutdown and cleanout once in a while. This should be done once or twice a year as a precaution, or as often as necessary, such as after a major outbreak of uncontrolled pests and diseases. A thorough cleanout also provides a good base for starting seedlings.


Cleaning a hydroponic system and indoor garden after all plants have been removed is a good opportunity to completely sanitize all surfaces as well as check equipment and make repairs. In hydroponic systems running hard water, lime scale and salts tend to build up inside irrigation lines, reservoirs and pumps.

Running the system with an acid solution for 24 hours will remove this buildup and is relatively safe, provided several rinses with water are carried out afterwards. This has the added benefit of helping to sterilize these surfaces.

The bases and tops of NFT channels, ebb and flow benches and any other constantly damp areas are likely to develop a layer of biofilm over time consisting of organic matter, dust, dirt, salts and bacteria, which can’t be removed by simply spraying with a disinfectant. Scrubbing is the best method of biofilm removal as it allows sanitation chemicals to come into contact with the surface beneath.

In greenhouses, a period of solarization during a system shutdown can be used as an extra degree of control over persistent disease spores or insect pests. This involves completely sealing the greenhouse and allowing the sun to heat the interior over a number of days.

The same method can be used to sterilize growing media. Simply place the media in a clear polythene bag and keep it exposed to the sun for a few weeks. For indoor gardens where solarization is not possible, leaving the hydroponic system void of plants for a couple of weeks will help eliminate many pests, but some disease spores can survive for extended periods of time with no host crop present.

Sanitation Compounds and Chemicals

Cleaning and sanitation methods fall into some basic categories. The non-chemical approach often just incorporates hot water and detergent, along with scrubbing and rinsing, which eliminates many basic problems without the need for stronger chemicals.

For stubborn grime, insect residues and sooty molds, using a baking soda paste can help as a scouring agent. An old-fashioned household cleaning mixture of sodium bicarbonate and citric acid or white vinegar is also suitable for cleaning a range of surfaces, including channels, tanks, equipment, walls and floors.

For sanitizing surfaces, such as the inside of irrigation lines and hard-to- reach corners, sterilization products are also required. These include readily available products that contain sodium hypochlorite (bleach), quaternary ammonium compounds, hydrogen peroxide or ethanol (70%).

Most of these cleaning compounds are not considered organic, but there are more and more organic sanitation products on the market for use in food-producing systems, each with advantages and disadvantages. Many growers prefer to use an integrated approach with more than one sterilization agent as part of an overall hygiene plan.

Household bleach is still one of the most commonly used disinfection agents due to its ability to kill off spores, bacteria and viruses when sufficient contact time is given. Bleach should be diluted down to a 10% solution with water just before use. Allow a contact time of 30 minutes in a well-ventilated area.

Bleach residues need to be thoroughly washed away before re-planting the system. The effectiveness of the bleach solution can be increased by mixing in a little dish detergent (a non-ionic surfactant), which helps remove more grime and acts as a wetting agent.

Other commonly used greenhouse disinfection agents may contain quaternary ammonium, which is less volatile and more stable than commercial-strength bleach. These products are highly effective and should only be used as indicated on the label.

Hydrogen peroxide, also called hydrogen dioxide, is another popular, easily obtained cleaning agent. It is a powerful oxidant and disinfection agent when used at the correct dosage (at least 200-300 ppm) and given a contact time of more than 15 minutes where spores and thick dirt have accumulated.

At this dose, hydrogen peroxide needs to be used when the hydroponic system is shut down and no plants are present, otherwise serious root damage can occur. Rinse it away, or leave it to dissipate over a period of days, as even small amounts of residues left after cleaning have could have a negative effect on sensitive seedlings. In addition to being used alone, hydrogen peroxide is also an active ingredient in a number of other cleaning products.

Ethanol is an effective disinfection agent most suitable for use as a dip or a wipe for pruning tools. Also use it during propagation and for wiping down surfaces such as benches and other small areas.

Since many serious plant pathogens, including viruses and bacteria, can be spread between plants on pruning and cutting tools, regular disinfection of these items is important. Ethanol is an effective sanitation agent but it is extremely flammable and is not really feasible for larger-scale disinfection purposes.

Water and Growing Medium Sterilization

Disinfecting of water and substrates, which come into contact with live root systems, requires particular care and attention, as residues of many sterilization agents—even at low levels—can damage sensitive young plants.

City water supplies generally don’t require additional sterilization agents, as water treatment chemicals are often added to meet drinking water standards, although hydroponic growers should be aware that the use of chloramines can damage younger plants.

Well water and other ground water sources may contain plant pathogens. It can be safely treated with UV, ozone, reverse osmosis, slow-sand filtration and hydrogen peroxide, provided all of the precautions are followed before the water is introduced into a hydroponic system.

For used substrates, steam sterilization is the safest method of disinfection, although any growing medium that contained diseased plants, particularly those infected with pythium, fusarium or phytophthora root rot, should be discarded and replaced with fresh, clean substrates.

Too Much of a Good Thing

While continuous sterilization and a high level of hygiene may seem to be the perfect answer to eradication and prevention of any infection from pests or pathogens, there can be a downside to overzealous disinfection. Not all microbes are pathogenic—the vast majority in horticultural systems are either benign or beneficial to plant growth.

The “kill everything” approach to running a completely sterile hydroponic system is an outdated idea. The objective these days is to start off clean and let naturally occurring levels of beneficial microbes develop, or even be introduced with inoculation products, to help suppress plant pathogens in the long term.

This doesn’t mean keeping a dirty system or growing area, but limiting the continuous use of sterilization chemicals that may leave longer-term residues. It also means choosing milder options when it comes to the complete system cleanouts, and avoiding the overuse of products that not only kill pathogens, but good microbes as well.

A clean, hygienic, well-run hydroponic system is not only pleasant to work in, it is one of the best forms of defense against pest and disease attacks.


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Written by Lynette Morgan | Author, Partner at SUNTEC International Hydroponic Consultants

Profile Picture of Lynette Morgan

Dr. Lynette Morgan holds a B. Hort. Tech. degree and a PhD in hydroponic greenhouse production from Massey University, New Zealand. A partner with SUNTEC International Hydroponic Consultants, Lynette is involved in remote and on-site consultancy services for new and existing commercial greenhouse growers worldwide as well as research trials and product development for manufacturers of hydroponic products. Lynette has authored five hydroponic technical books and is working on her sixth.

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