How to Sanitize and Sterilize Your Hydroponic System?

Created by
Added 26 July 2023

When was the last time you sanitized and sterilized your cannabis hydroponic system? Before growing your current batch of cannabis plants? Then, It may not be too late. 

But if you don’t remember doing that, your cannabis plant may be in trouble. 

Cannabis is a hardy plant but it is still prone to diseases and growth problems if the growth conditions are not right. And dirty hydroponic setups are the first step in worsening growth conditions, and they can lead to many problems. 

So, in this article, we dive into how you can sanitize and sterilize your hydroponic setup and turn it into a clean space for your cannabis plants to flourish. Read on to know more. 

Why Do You Need to Sanitize and Sterilize Your Hydroponic Setup?

Why Do You Need to Sanitize and Sterilize Your Hydroponic Setup?

Your hydroponic setup not only houses your cannabis plants, but many other organisms, including pests, pathogens, and sometimes, even fungal spores. Over time, these microbes can grow in numbers and pose a significant risk to your cannabis plant. Let these microbes flourish in your hydroponic system and you’re inviting various problems. Here are a few reasons why you should sanitize your hydroponic setup:

1. Prevent Disease Spread

Hydroponic systems allow you to control the environment but they can also be a perfect breeding place for pests. Many pests, including fungi and bacteria, can multiply rapidly, thanks to the humid and warm environment. If you don’t pay attention, these pests can contaminate the roots, stems, and leaves of your plants resulting in diseases that can affect the entire crop. Sanitizing and sterilizing the system helps eliminate these potential threats and reduces the risk of disease outbreaks, protecting your investment and hard work.

2. Preserving Plant Health

Healthy plants are much more resistant to pests, stress, and many other diseases. If your hydroponic system is tidy and free of contaminants, your plants can use all their energy to grow healthy and produce big buds. In addition, healthy plants are more likely to absorb nutrients efficiently, so the healthier they are, the more yields they produce. 

3. Preventing Algae Growth

Algae can be an annoying issue in hydroponic systems, specifically when there is adequate light and nutrients. Although it doesn't compete with the plants for nutrients, it can clog your equipment and minimize the efficiency of the system. By sterilizing the system and managing algae development, you make sure that your plants get the nutrients they require without unwanted issues.

4. Preventing Nutrient Imbalances

Organic matter, decaying plant material, and other debris left in the hydroponic system can decompose over time and affect plant health and yields. By this logic, sterilizing your system can help you prevent nutrient discrepancies and ensure that the nutrient solution remains consistent and appropriate for the plants' needs. 

5. Minimizing Root Diseases

Root-related problems such as root rot are prevalent in hydroponic systems. Also, there could be mold and fungal infestations around your hydroponic setup, like bud rot, slimy roots, etc. This is because roots are almost always in close contact with water and are vulnerable. However, if you sanitize and sterilize the system frequently, you can decrease harmful microbes in the root zone and promote healthier root growth and minimize the risk of root-related problems.

6. Longevity of Equipment

Maintaining your hydroponic equipment can prolong its lifespan considerably. Mineral deposits, algae buildup, and residues from organic matter can clog pumps, tubing, and other components, reducing their efficiency and eventually leading to equipment failure. Therefore, clean and sanitize your equipment regularly so everything runs smoothly. 

7. Better Water Quality

Clean systems contribute to better water quality. An unhealthy substrate leads to nutrient problems for your plant. Since the plants are going to absorb the water directly, it will help to remove all contaminants and supply them with a clean nutrient solution.

8. Optimal Oxygenation

Oxygen is important for healthy and balanced roots in hydroponics. Lack of oxygen can create anaerobic conditions that eventually produce hydrogen sulfide, causing the grow room to reek. A clean system with unrestricted flow not only enables much better oxygenation of the nutrient solution but also minimizes bad odor. Sufficient oxygen levels in the roots help with growth, nutrient uptake, and plant vitality.

These are just examples of what could happen if you don’t sanitize and sterilize your hydroponic setup often. An unclean hydroponic setup and grow room are like a ticking time bomb — a disaster waiting to happen. And ongoing maintenance and cleaning can help diffuse this time bomb before it even starts ticking. 

What is the Difference Between Sanitization and Sterilization?

What is the Difference Between Sanitization and Sterilization?

Cannabis plants prefer slightly warm conditions, which is also the thriving ground for other pathogens, pests, and fungus. This is where sanitization becomes a crucial step in maintaining your hydroponic setup as it helps you prevent the risk of contamination and infestations in your cannabis garden. 

The goal of sanitization is to clean your hydroponic setup and growing space by removing all the dirt and debris that may attract such pathogens, pests, or fungus. Generally, this is more than enough for most growers, but sometimes, you may need to take this a step further with sterilization, whose goal is to eliminate all living organisms within the hydroponic setup. 

As cannabis growers, the difference you should consider between the two terms is that sanitization is about cleaning your hydroponic to the T, and sterilization is killing off all the pathogens in the grow room. Do note that this is not the official differentiation; according to the CDC, sanitization occurs when 99.9% of microorganisms are eliminated and sterilization is when 99.999% of microorganisms are eliminated. Obviously, you don’t need to worry about the numbers; instead, do the best you can. 

Things You Need for Sterilizing and Sanitizing Your Hydroponic Setup

Things You Need for Sterilizing and Sanitizing Your Hydroponic Setup

It’s time to disinfect your hydroponic setup, but before you start, you need to get the right supplies. Cleaning a hydroponic setup isn’t as easy as running a microfiber cloth over your TV, it requires meticulous planning and specific supplies because a hydroponic system is ripe with dirt, salts, microbes, and much more. You need the right tools and cleaning agents, which are as follows.

1. Sponges and Scrubbers

Your hydroponic setup is largely made of plastic, and sponges are the best choice when it comes to cleaning these plastic components. A sponge is better than a cloth because it holds the soap well while being soft and easy on the components, and it can help you get in tight corners. You can use any regular soft sponge, even the one that you use to wash dishes. 

You also need to get scrubbers because sponges, as good as they are, are only effective at cleaning soft debris. For hard debris like mineral or salt buildup, you need a scrubber to get everything off effectively. 

A hydroponic system is often a network of plumbing, and the pipes can be a pain to clean with sponges. So, it’s also a good idea to get some bottle brushes that can help you clean the insides of the pipes. Get a moderately hard bottle brush to clear up all the buildup and debris from within. 

2. A Vacuum Cleaner

The next thing you need is a vacuum cleaner; it’s not a must but highly recommended as it can make cleaning filters, tents, and vents super easy to clean. A regular indoor or car vacuum cleaner is more than enough unless you have a cannabis farm to clean up. This device can help you clean dry dirt, dried leaves and other plant matter, spider webs, and some stray pests. 

3. Compressed Air

Along with a vacuum cleaner, it’s also a good idea to get some compressed air cans, which come in handy while cleaning tight corners in your hydroponic setup. These can help you clean hard-to-reach places but are only effective against dry things like electrical parts or other components that can’t be exposed to moisture. 

4. Scissors 

Scissors because you’ll have to cut up all the zip ties holding your hydroponic setup in place, but that’s not all you want scissors for. We recommend getting scissors to prune your cannabis plant so it does not shed so much organic matter in the following weeks, which is a major reason for debris in your grow room on rent. 

5. Cleaning Agents

Things start to get serious when we come to cleaning agents, which are solutions that will help make your hydroponic setup squeaky clean. There are many options you can choose from, which are as follows. 

Food Grade Hydrogen Peroxide

Hydrogen peroxide is one of the best hydroponic system cleaners for cannabis growers, and it is available in a variety of concentrations. However, for hydroponic setups, ensure the hydrogen peroxide you get is less than 35%, which is also known as food-grade hydrogen peroxide. 

You can find these in most online stores and they are relatively straightforward to use. You have to dilute the product in water, as recommended by the manufacturer, and scrub the surfaces with it to clean them. That’s it. 


Bleach is another product that can sanitize hydroponic systems quite well, and it is even easier to find than hydrogen peroxide. However, you shouldn’t use bleach powder in your system — you don’t want it to end up on your cannabis plant. Instead, you need to be particular about how to use bleach to clean your cannabis hydroponic system. 


A product that you may already have in your kitchen, vinegar, is also quite effective at cleaning hydroponic systems. Like hydrogen peroxide, vinegar is also easy to use. Dilute it in lukewarm water (or boiling water for hard salt buildups) and wipe down the components with it. 


Lysol is often used to clean glasses and tables, but it can also work to clean your hydroponic system. This disinfectant solution is designed to clean non-porous surfaces and is usually safe on electronic equipment, too. Lysol can ensure your hydroponic setup is completely germ-free!

Sterilizing and Sanitizing Your Hydroponic System 

Sterilizing and Sanitizing Your Hydroponic System 

Now that you have all the cleaning supplies ready, let’s move on to cleaning your hydroponic system. Ideally, you want to do this between crop cycles or when you think your hydroponic system is too dirty. If you clean your hydroponic system during a crop cycle, the cleaning agents may stress out the plant, so you must be careful and gentle. 

Follow these steps to sterilize and sanitize your hydroponic system. 

1. Drain the Reservoir

The first step whenever cleaning your hydroponic system should be to drain the reservoir and remove all the water from the setup. To do this, stop the pump, drain the reservoir, and dismantle all the pipes so there is no waterlogging anywhere in the system. 

If you’re using a recirculating hydroponic system, use a hose to run water through the entire system — this will remove all the dirt and debris from the pipes and collect them into the reservoir. While it won’t work against salt buildup, let’s save that for the next step. 

2. Clean the Salt Buildup 

Salt buildup is quite common in hydroponic systems, especially if you use high concentrations of nutrients or tap water. But it’s relatively easy to clean! All you need is vinegar. 

Soak the surface with salt buildup in vinegar for at least an hour, so all the salt can dissolve properly. You can also scrub the surfaces with a sponge dipped in vinegar or spray down components with a spray bottle. 

After an hour, rinse all the components with water multiple times to remove all the dissolved salts and vinegar from them. This step is crucial! Always rinse at least two to three times. 

3. Clean the Rest of the System 

The next step is to clean everything else on your hydroponic system. Here, it is recommended to use one or two cleaning agents at most, nothing more, and always keep the chemical compositions in mind. 

Start by creating the right cleaning agent. If you are using food-grade hydrogen peroxide, mix 3 ml of the product with a gallon of water. In the case of bleach, mix 40 ml for a gallon of water. 

But before you use the cleaning agent, ensure you have already removed all the dirt and debris from the system. Then, use a brush or sponge to clean it thoroughly. Once all the components are cleaned, you can start disinfecting them with the cleaning agent of your choice.

Fill your reservoir with the cleaning agent, either hydrogen peroxide or bleach, and ensure you fill the reservoir higher than you normally would. Next, run your hydroponic system and let the cleaning agent circulate through your setup for at least five hours. You can run it for longer if your system is more complex or big. 

Meanwhile, you can dip other components in the solution in the reservoir and use a scrubber to sterilize them. If you do this properly, you will disinfect and clean each and every corner of your hydroponic system, but there’s some more work to do. 

The cleaning agent you used is effective but it is also dangerous for your cannabis plant. So, you need to remove every trace of it from your hydroponic system. Start by draining the solution from your setup, and clean the reservoir with water. 

Then, refill the reservoir with fresh water and recirculate it through the setup for a few hours to thoroughly rinse it. Drain the system again and wipe down everything with a clean cloth. Once the system is dry, you can refill it with fresh water. 

4. Take Care of the Peripherals 

Finally, you need to clean all the peripherals of your hydroponic system, like grow lights, fans, vents, etc. These areas do not come in contact with water but can still harbor spores, dirt, and pests. So, clean all the components with Lysol and a sponge thoroughly. 

Lysol is effective but only use it on non-porous surfaces and exteriors. Do not spray it directly on the grow lights or fan motors. Instead, follow the manufacturer’s recommendations on cleaning the nooks and crannies of each peripheral. Generally, this would involve using contact cleaning sprays, cloth, alcohol wipes, etc., depending on the component. 

That’s it. Your hydroponic system is clean, sanitized, and disinfected. Move your plant into it and let it flourish. 

Tips for Cleaning Your Hydroponic Setup for Cannabis

Tips for Cleaning Your Hydroponic Setup for Cannabis

Your hydroponic system may be as clean as a freshly bathed kitten, but you need to ensure it is cleaned thoroughly and stays clean for the next crop cycle. So, use these tips. 

1. Add Hydrogen Peroxide to the Nutrient Solution 

If you want to keep your hydroponic system clean for longer, you should consider adding 3% diluted hydrogen peroxide to the nutrient solution, which will keep the system clean without harming your cannabis plants. 

Experienced growers recommend adding 10 ml of 3% hydrogen peroxide to a gallon of water in the nutrient solution, and adding 15 ml more every few days. But the use of hydrogen peroxide is often debated, so do your research and decide if using it is the right way for you.

Also, if you introduce beneficial bacteria to your cannabis plants, avoid hydrogen peroxide as it can kill friendly bacteria, too. 

2. Sterilize Gardening Tools After Every Use

Additionally, you should also sterilize your gardening tools after every use to ensure your hydroponic setup stays clean for longer. Gardening tools, especially knives and scissors, cut into plant matter and, if they are dirty, they can contaminate the plant. 

So, once you are done using the tools, dip them in isopropyl alcohol to remove all the sticky debris from the tools and disinfect them. For tools like pH and EC pens, follow the manufacturer’s recommendations to clean them and prolong their life and accuracy. 

3. Clean Your Hydroponic System Regularly

There’s a lot of debate about how often a grower should clean the hydroponic system, but ultimately, it depends on you — how often do you want to clean your hydroponic system?

You can clean your hydroponic system as frequently as twice a month, but honestly, that would be a waste of time, energy, and nutrients. On the other hand, only cleaning it once a year will invite trouble for your cannabis plant. Even the size of your hydroponic system comes into play here. 

As a general rule of thumb (read: for starters), clean components like pipes, pumps, and reservoirs every time you change the nutrient water. If you top off the water, you should replace the water once it has been fully cycled. 

All the other components should be cleaned when they are visibly dirty or at least in two months, whichever comes earlier. Again, the frequency may vary depending on your setup. And there is no right or wrong answer to this. Grow enough hydroponic plants and you’ll figure out what needs cleaning and how often. 

4. Always Follow the Manufacturer’s Recommendations 

Whether it is about preparing your cleaning agent or cleaning a particular component, always follow the manufacturer’s recommendations. They know best. Every other tip mentioned in this guide is generic, but may not work for your specific components. 

Also, this tip becomes more than crucial for mixing cleaning agents. They are harmless as long as you use them correctly, but if you mix them with something else or use higher concentrations than recommended, it’s an open invitation to trouble for you and your plants. 

5. Do Not Compromise Safety 

Cleaning may seem harmless and easy, but it is recommended that you wear safety glasses, gloves, and a mask when working with cleaning agents. Some cleaning agents, like hydrogen peroxide, can cause irritation to the skin and eyes, so it is always a good idea to practice safety even if you’re using dilute agents. 

Along the same lines, never mix chemicals, especially bleach. For example, mixing vinegar and bleach creates chlorine gas, which is harmful to us. Mixing agents will not make them clean better, but it can make them more dangerous for you and your plants. 

6. Always Use Food Grade Hydrogen Peroxide 

Always make sure you only use food-grade hydrogen peroxide on your cannabis plants. It is safe for your plant and yourself. Do note that even 35% food-grade hydrogen peroxide can still irritate your skin, so you need to dilute it with water in a ratio of around 1:11. 

7. Don’t Use Bleach All the Time

Think of bleach like a gun, and you don’t want to bring a gun to a knife fight. It is no doubt effective at sterilizing things, but it is also harsh and should not be used when the plant is still present in the setup. It can seriously hurt your cannabis plant. 

So, only use bleach when the hydroponic system is free of plants and you are dealing with a major salt buildup or disease outbreak. And make sure you rinse your setup thoroughly after using bleach. 

8. Maintain the Right Nutrient Solution Temperature

One of the most underrated tips for keeping your hydroponic system clean is maintaining the right temperature in the reservoir. Ideally, stick to a temperature between 65°F to 75°F (18°C to 24°C). High temperatures lead to low oxygen, which is bad for root development, and cold temperatures can cause cold stress to the plant. You can use aquarium radiators or heaters to regulate the nutrient solution temperature. 

9. Check the Filters 

Always keep an eye on the filters as they are the most prone to getting dirty quickly. They are constantly filtering dirt and pests, so if they get too dirty, they can become less effective at their job. So, check and clean the filters as soon as they look dirty. It takes five minutes to clean the filters but doing so will go a long way in keeping your overall grow room clean and free of debris and pests. 

Summary: How to Sanitize and Sterilize Your Hydroponic System?

Your cannabis plant deserves a clean hydroponic system to thrive in, and even though your hydroponic setup may look clean to your eyes, it may be harboring bacteria and many other pathogens. This can lead to problems like pest infestations, mold, diseases, and much more for your cannabis plant. 

So, get your supplies ready and prepare the cleaning agent. Start by draining the reservoir, flushing the hydroponic system with the cleaning agent, and scrubbing down other components with the suitable cleaning agent. And don’t forget to rinse it for a few hours with fresh water to remove any trace of the cleaning agent. 

Follow these steps and other tips mentioned above and your hydroponic system will be cleaner than it was on Day 1. 


Be the first to comment it