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How to disinfect hydroponic system

How To Disinfect Hydroponic System?

    Want to know how to disinfect hydroponic system right way?

    All you need is the right things to clean, and proper knowledge of how to use them. 

    Also if you know which are the areas you need to clean, you can keep your hydroponic system clean. 

    This is exactly what we have compiled in this post.

    Let’s get started!

    Things Required to Disinfect Hydroponic System

    In order to disinfect the hydrophobic system, you would need the right things to clean it perfectly.


    Well, due to the use of water and different nutrients in hydroponic systems, it is exposed to the salts, microbes, and dirt build up. 

    To clean each build-up you would require different tools, cleaning agents, and treatments.

    Let’s look at all tools  you need to disinfect a hydroponic system: 

    1. Sponges

    The hydroponic system uses several parts that are made up of plastic.

    In order to clean these plastic parts, sponges are the best. 

    Use any cleaning agent like soap with little water and scrub the surfaces. 

    You will be able to clean the dirt with ease.

    It is much better than using a piece of cloth. 

    You can get any regular cleaning sponges that you use in the kitchen. 

    2. Scrubbers

    Sponges are fine when you’re concerned only about bacteria, fungi, and other microbes.

    But cleaning mineral build-up requires something rough like scrubbers.  

    Using scrubbers you can remove salty scales much effectively.  

    3. Bottle Brushes

    The hardest place to clean in a hydroponic system are pipes. 

    You must make sure they are clean because pipes are the ones that supply water to the crops.

    For cleaning hydroponic system pipes, you can use bottle brushes. 

    Using it you can brush the insides of the pipes. 

    It is effective against cleaning salt build-up, fungi, algae, and dirt. 

    4. Vacuum Cleaner

    A vacuum cleaner is not required most of the time but it can be useful if you want to clean air filters, grow tents and vents. 

    Any small or medium capacity vacuum cleaner will do the job.

    Using vacuum cleaners you can clean out dry dirt, spider webs, dried leaves, dried flowers, etc. 

    5. Compressed Air Cans

    Compressed air cans are useful when you need to clean tiny nooks and corners. 

    Mostly you will be able to clean the dry stuff out of these unreachable areas.

    Also, you can use it to clean electrical parts or systems which otherwise you cannot clean with water or other liquid cleaning agents.

    7. Scissors and Cutters

    Cleaning dirt builds up, microbe buildup, or salt build doesn’t ensure that your hydroponic system is clean. 

    You have to remove the things that can lead to these build up. 

    Usually, shedding of leaves and flowers is the major cause of this build. 

    Regularly remove dried leaves and flowers of the plant.

    For that, you can use scissors or cutters. This can be any gardening cutters or scissors. 

    Make sure you keep an eye on drying leaves or flowers. 

    Once you are sure the part is dried, immediately cut it. 

    In addition to these tools, you will need proper closing agents so that you can effectively sanitize and sterilize the complete hydroponic system. 

    Here is the cleaning agent that you can get depending on what system you use and what you want clean:

    1. Food Grade Hydrogen Peroxide

    Hydrogen peroxide is the hydroponic system cleaner that you can use.

    Hydrogen peroxide is available in various strengths but since you want to use it for hydroponic systems, it should be less than 35 percent hydrogen peroxide. 

    It is classified as the food grade hydrogen peroxide. 

    They are readily available in most of the online stores. 

    We recommend you to go with something like Brio Super hydrogen 12% hydrogen peroxide

    Just dilute it with water and wipe the surfaces. Leave it for 5-10 minutes and then you can clean with some kind of wipes. 

    2. Bleach

    Another cleaning agent that is suitable for sanitizing hydroponic systems is bleach. 

    Bleaching powder is readily available in most of the stores as a cleaning agent. 

    You may not be able to use the bleaching powder for the hydroponic system as you do it while cleaning the kitchen.

    You do not want bleaching powder to go into the system and adversely affect the plants. 

    So you must know how much to use and how to use the bleach for cleaning hydroponic system.

    Don’t worry! You will learn more about the use of the bleach in this post. Just keep reading.

    3. Lysol

    Lysol disinfectant is another great choice if you want to clean hydroponic system. 

    It is available in the form of sprays. 

    And it is specifically designed to kill germs and viruses on non-porous surfaces. 

    You can even use it on electronic equipment as well as the different surfaces. 

    It could be a good option when you want to prepare the system for a new plant. 

    Clean everything with Lysol and the system is germ-free for new crops. 

    4. Vinegar 

    If you do not want to buy some chemicals from the market and need something that is available right in your home, vinegar is the best cleaning agent for your home hydroponic system. 

    You can mix the vinegar with some lukewarm water and just wipe the surfaces. 

    If you are dealing with some tough stains and build up,  just boil this mixture of water and vinegar, and then wipe the build-up. It would come off easily. 

    How To Disinfect Hydroponic System?

    Lets look at in detail how to clean hydroponic system effectively.

    Once you have the right tools and cleaning agents, you must know the proper process to clean the hydroponic system. 

    Firstly, always clean hydroponic system whenever you are preparing for the new crop. 

    The best time is right after the harvest as there is no plant.

    If you clean the system when there is a growing plant, the cleaning agents or chemicals can cause stress on your plant. It may even kill the plant.  

    Hence it is wise to learn a little how-to disinfect the hydroponic system in a proper way. 

    We have divided the complete process into steps. 

    It is possible that some things might change depending on the nature of your hydroponic system but the steps remain the same. 

    Step 1: Remove the Water

    The foremost step in this process is to first drain all the water from the system. 

    Stop the water supply from the pump and also empty the reservoir of the system.

    Also, dismantle all the pipings and fittings to make sure there is no water logging in the system. 

    This method of removing water is suitable for the simplest of hydroponic systems.

    One thing you can do if you have a recirculating hydroponic system is to run water using a hose through a complete system to make sure any debris or dirt is also removed.

    With this step, you must make sure that all the water that was used in the system is removed along with the debris and minerals. 

    At this point don’t worry about the salt build-up or the hard to remove substances. 

    Step 2: Cleaning Salt Build Up

    When you are using tap water in the system,  it is quite possible after some time there will be a salt build-up.

    This is the most common problem of all hydroponic systems.

    It has a very simple solution.

    Use vinegar!

    All you have to do is soak the surface that has salt build-up with vinegar. 

    All it soaks for atlas 30-60 minutes to make sure the salts are dissolved. 

    Some even like to keep full-strength vinegar in a spray bottle.

    Using a spray bottle you will be able to apply the vinegar more effectively.

    After an hour or so of applying vinegar, rinse it with water.

    Rinse the system twice or thrice to make sure there is a trace of vinegar.

    Step 3: System Cleaning

    Every time you harvest a crop and prepare the system for the new one you must sterilize the whole system.

    At this stage, I would advise you to use one or two chemicals to disinfect the system but be careful. 

    Just keep this chemical composition in mind:

    • For one gallon of water mix only 3 ml of 35 percent for grade hydrogen peroxide.
    • In case you are using bleach, use 35- 40 ml of bleach for one gallon of water.

    Before you start disinfecting the hydroponic system, make sure that you have removed the dirt and debris from the system.

    Usually, you will find some dried leaves, roots, slime, etc. Clean everything with a scrubber or a brush. 

    Use a bottle brush for areas where it is not easy to reach. 

    Once you are sure about the fact that you have removed everything that is visible, it’s time to remove the things that are not visible. 

    Disinfect the whole system!

    Follow these simple steps to make sure that your hydroponic system is completely bacteria-free.

    1. Fill in your hydroponic system with the chemical composition that we described earlier. Use either a bleach solution or a hydrogen peroxide solution.
    2. Make sure to fill the system with a solution to a level that is higher than you usually fill using the regular water. This will help you cover the areas where generally algae build up occurs.
    3. Next, is to run the system and let it circulate the solution for 5-6 hours. If the system is big, you can run a little longer. 
    4. While the system is running, use the sterilized scrubbers or brushes to clean areas like flood trays, pipes, etc. 
    5. Also use the same solution to clean external areas like lids, hoses, etc. as the circulating solution won’t be able to reach there. 

    If the process is followed properly you will be able to remove all kinds of visible or invisible things from the system. 

    But you are not done yet.

    You have treated your system with a chemical that is dangerous for any plant, hence you cannot use the system yet.

    You will need to remove the chemical completely from the system. Especially, from those areas related to the water circulation system. 

    Don’t worry you don’t have to do anything. 

    Drain the cleaning solution out of the system completely. 

    You will notice that there is some residue in the reservoir if you are using any. Make sure to remove the residue and clean the tank with water before going to the next step.

    Now fill the system with fresh, neutral water and recirculate it in the system for a few hours. 

    If you want you can change the water a couple of times to make sure there are no traces of chemical agents. 

    Once, you are done, just drain the system again. 

    Now use clean wipes to wipe off the water. Make sure to dry off every part of the system. 

    A cool trick I use to remove the droplets is to turn on the HID lights and if you don’t use such lights, even a hair blower will do the trick. 

    Step 4: Taking Care of Other Areas

    Even after you have applied all the steps that we mentioned up till now, there is some possibility that your system is yet 100 percent clean.

    You need to clean even those areas that do not come in contact with water or the plant. 

    This could be anything from the exterior of the pipe, lighting systems, fans, and other electrical or electronic systems.

    This where you can use a cleaning agent like lizol.

    Use the regular Lysol spray in order to clean the different parts of the hydroponic system.

    Remember to use the spray only one the non-porous surface. 

    Avoid using air stones like coir, clay pebbles, etc. 

    We would advise you to use Lysol only for cleaning the exterior surfaces like the exterior of the water tank or the body of electronics or electrical appliances.

    Important Areas You Need To Sanitize In Hydroponic System

    You understand the process of cleaning the hydroponic system,  but by knowing the areas that you would have to disinfect it would make your effort effective. 

    Here is the list of all three areas that you would have to disinfect.

    1. Plant Pods

    For growing plants, you might be using some kind pods like net pots. 

    You must remove all the dead roots after harvesting and clean it with vinegar or lysol to completely disinfect it.

    If you see there is a lot of waste attached to nets, you can soak it in water and later remove the debris with an appropriate brush. 

    We recommend you to replace the net pot if you feel it is deteriorating. 

    You can buy heavy-duty net pots like Cz Garden Supply 3 inch Net Pots from Amazon. 

    2. Surfaces

    There are several surfaces and walls that are exposed to the hydroponic system. 

    These surfaces include walls of pipes, lids, walls of reservoirs, sensors, and other fittings.

    We have already described how to clean these surfaces. 

    All you have to do is segregate areas that need chemical treatment and simple scrubbing. 

    In case you are using some kind of sensor you do not want them to be exposed to chemicals.

    Clean them with a clean cloth. It is more than enough.  

    3. Lights

    In case you are growing plants indoors,  you might be using artificial lights for your hydroponic systems. 

    Though the light fitting is not directly in contact with the crop or water,  it does become a source of dust. 

    The dust is not that harmful but over an extended period of time, it could lead to fungus or bacteria. 

    So it is wise to remove it before it leads to that. 

    Use a simple cloth to clean these lights. We suggest using a vacuum cleaner if you want to clean it nicely.  

    4. Air intakes and outlets

    Air take is the place that brings most of the dust into the system. 

    Especially the hydroponic system using grow tents, get unwanted entities through air filters.  

    Most of the filters do use dust and bacteria filters but if not cleaned regularly, the filters become a source of pollution for the hydroponic system. 

    Simple cleaning measures won’t work with these filters.  

    You will have to open the filters and vacuum them properly. 

    In case you are using air conditioners, clean them regularly. 

    You can get plenty of videos on cleaning the air conditioners on YouTube.

    Some air filters are washable, you can soak them in water with a little mixture of vinegar and water.

    Just like you did in step 2. 

    Or you can use hydrogen peroxide as we mentioned in step 3.

    Cleaning hydroponic system with hydrogen peroxide will solve lot of build up issues.

    Also change the filters, if they are compromised in any way because you do not want to contaminate the system when you are growing a crop. 

    5. Electrical or Electronic Devices

    You also want to take care of your electrical or electronic devices used in the hydroponic system.

    Any dust or salt build-up can reduce the efficiency or worse, it can cause the device to malfunction.

    Since it is an electronic device you do not want to use any kind of wet cleaning agent.

    Simply use a dry cloth to clean the dirt or dust.

    There is something called electrical contact cleaner which you can use to clean all the electrical plugs, pins, or connections.

    You can buy WD-40 Specialist Electronics Maintenance Trio which is specifically made for cleaning electrical or electronic devices.

    6. Reservoir Tank

    If you ask me what is the one part of the hydroponic system that you want it to be clean.

    Without a doubt, it has to be a reservoir tank.


    Since water is the main medium that carries required nutrients and minerals for the crops, you do not want it to be also supplying unwanted entities.

    you can carry out all the steps from 1 to 3 in order to clean the reserve tank completely.

    Final Thought

    The method on how to disinfect hydroponic system that I have mentioned in this post is applicable to all kinds of hydroponic systems. 

    However, it is only used when you are planning to plant new crops.

    If you have any alternative methods or unique methods that you use for your hydroponic system feel free to share. 


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