How to Clean Hydroponic Tubing


The success of a hydroponic system is only as good as its upkeep and upgrades. As with all living things, a poorly-maintained environment will cause health deterioration and in worst-case scenarios, decay and death if not properly attended to. Therefore, this applies even more relevantly to hydroponics because it’s growing plants in sterile environments along shared troughs of nutrient water solution in close proximity. A measly bacterial or pest infection would spread like wildfire and spell doom for your entire system very quickly. 

To prevent such a catastrophe, many hydroponic gardeners/farmers are therefore more meticulous than traditional ones. Their typical sanitization goes beyond to the extent of sterilization.

Sanitization vs. Sterilization

While similar in concept, they actually differ considerably in their approach. 

Firstly, you may consider sanitization as the primary aspect preceding sterilization. Essentially, it refers to a continuous upkeep of the state/condition of your hydroponic system by cleaning and tidying it regularly. It includes disposing of all unnecessary waste products such as dead or decaying plant matter, filthy air pumps, and so on. Since hydroponics utilizes a connected system, an initially isolated area of filth will quickly spread to all plants present within the same tube and eventually, the entire system. This will result in the system becoming a massive breeding ground for diseases and pest infestation. 

Secondly, sterilization refers to a more comprehensive ‘wipe-down’ of your whole hydroponic system. This includes both the gardening plot holes and the physical, mechanical components of it. It requires the utilization of more heavy-duty appliances and chemicals to kill off more resistant or stubborn microorganisms that might have otherwise been missed during the initial sanitization. Consistent, systematic sterilization will help prevent unwanted systemic infections to your system in the long run. Hence, it’s ideally recommended to perform this after each harvest when your system is introduced to a plethora of pathogens from the outside air/surroundings.

To facilitate these two processes, you’ll need a wide variety of tools: sponges, scrubbing brushes (large and small), mop & bucket, rubber gloves, goggles, clippers/scissors, cleaning rags, wet/dry vacuum, compressed air cans and a garden hose with female hose adapter. These are just among the few essentials to start you off with. With regards to cleaning agents, you might want to consider chemicals like bleach, vinegar, isopropyl alcohol, or even hydrogen peroxide. They are all strong chemical reagents to effectively eradicate germs.

Words of Caution

Some useful advice would be to always read the label. It is your personal responsibility to be informed and aware of the potential dangers of using each tool or chemical. You should never rely on your own intuition or assumption if it’s unfounded. The health and safety information booklets or manuals are always provided and available for your perusal. Health and safety comes first. With that in mind, always ensure to be properly attired and geared up appropriately in rubber gloves and safety goggles to prevent occupational hazards or unforeseen blunders arising from ill-handled equipment and chemicals.

When it comes to handling chemicals, always be alert and never mix them together. Be well-informed of their differing concentrations and their relevant effects. Naturally, the higher the concentration, the more potent it will be. An exceedingly high concentration would undoubtedly become toxic to your plant and the system. Thus, refrain from adding any chemical in high concentrations. It should always be added in milder ratios. For example, food-grade hydrogen peroxide has a concentration of 35%. Despite its label of ‘food-grade’, necessary precautions should always be taken because it will burn the skin if exposed. Diluting it down to 3% will make it safer for use. 

The Multifaceted Hydroponic System

As mentioned previously, cleaning your system in between harvests is the most ideal. It prevents unnecessary stress on your plants and allows you to compartmentalize each area for cleaning. However, if you have outstanding plants remaining in the system, ensure to either remove or transfer them prior to a separate nutrient solution similar to the preexisting one so they won’t perish during your cleaning. 

Following this, a general rule of thumb to begin the sterilization process would be to adopt an up-down approach. Working from down-up would just cause dust from the upper flanks to fall down on the cleaned lower flanks, thereby negating your efforts. 

Target walls and work surfaces first. Scrub them meticulously using the chemical solution of your choice — either diluted hydrogen peroxide or vinegar. It’s recommended to perform this wipe-down twice to be thorough.

Once you’re done with the tangible surfaces, you can focus on lights next. It’s a common rookie mistake of many new farmers and gardeners to neglect them. They forget that these areas also accumulate a lot of dust and germs which can fall onto your plants. They can be easily prevented with a simple wipe-down using a damp cloth. For further sterilization, use isopropyl alcohol to avoid leaving residues or streaks. Also don’t forget to clean the electrical areas surrounding the system using an air compressor to blast out all the dust. 

Last but not least, take care of your air intake filters too. They should be cleaned at least monthly in order to maintain or improve their efficiency. Such regular maintenance facilitates fresher air intake into your hydroponic system. 

Step-by-step Approach

While we have previously explained the generic top-down process advised for the cleaning process, here’s a brief overview of the procedure.

(a) Drain the System

This can manifest in two approaches: the Return Pump method and the Drain Valve method. 

(b) Cleaning Process (Pre-Sterilization)

Adequately rinse the components of your system before cleaning your system thoroughly. Ensure that your sterilizing chemicals are very diluted before using. 

Remove any air stones and do a rough sweep of your system for any debris or decaying plant matter. Proceed then to use the sterilizing solution to wipe down all exposed surfaces. Change your ¾ inch hose before you fill-up the whole system to regular depth with a mixture of water and the sterilizing solution. Allow this newly-concocted solution to sit and circulate within the system for about four to six hours. Afterward, drain the water and begin scrubbing intensely to get rid of any remaining stubborn germs, especially in the nooks and crannies of the channels (PVC pipes). Finally, use a slender bottlebrush to scrub the more inaccessible joints and areas leftover in the system.

(c) Sterilization

Once you’ve completed the initial cleaning, you can proceed with the subsequent sterilization by targeting each system component individually. This includes your pumps, pots, and growing medium. Hydrogen peroxide is recommended at this stage.


Although this guide is far from comprehensive, its main objective was to educate any readers new to the world of hydroponics on the importance and the nuances of the cleaning process. We hope that it’ll be beneficial in helping you initiate the process of sanitizing and sterilizing your system appropriately. Knowledge is power and when used together with the relevant tools/equipment, you’ll be able to set yourself up for success.


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