How to Clean Your Hydroponic System


Growing your own food indoors using hydroponic gardening systems offers many advantages. Primarily, you will usually yield healthier plants faster. The indoor environment offers your plants a safe and protected sanctuary where ideal growing conditions can be achieved.

Yet, despite the many benefits of hydroponic growing indoors, as the grower you must still be conscious of investing the appropriate amount of cleaning time into the system itself. An unclean system will over time damage your plants’ health due to the potential build-up of algae, mold and bacteria. If left unmaintained, your system can essentially become a breeding ground for harmful diseases and will eventually destroy your crops.

The best way to deal with this potential problem is to take preventative measures. This means you’ll need to get into a routine of cleaning your hydroponic system regularly. By cleaning your hydroponic system consistently, it makes the job far less difficult each time as you’ll be staying ahead of the curve.

4 Steps to Clean Your Hydroponic System

Here are some simple steps to ensure proper cleanliness of your hydroponics system:

1. Remove Plants

Start off by removing your plants from the hydroponic system. Transplant them into a separate container, ideally with the same grow medium, nutrient solution, and pH levels. Replicating the plants’ home is the best way to ensure your plants don’t go into shock when taken out of their environment.

2. Sterilize the System

You’ll want to clean your hydroponic system’s reservoir and the parts by flushing the system with a cleaning agent. There are hydroponic cleaning solutions available at your local hydroponic shop or online. Many growers also opt to use a diluted bleach mixture to flush their hydroponic system. This may raise concerns with some individuals, therefore choosing natural cleaning products is also another good option.


A recirculating hydroponic system can be flushed with a cleaning solution regularly. Image via Plant!t Professional Growing.

3. Soak and Rinse

After the system has been flushed with the cleaning solution for approximately 24 hours, you’ll want to rinse it out with pure water. Circulate filtered water through the system for at least one to two more 15-minute cycles. Discard the water to wash away any remaining cleaning solution residue.

4. Replanting

After you’ve flushed and rinsed your system, you can begin to return your plants into their home. Re-establish your grow medium and activate your system as normal. Monitor your plants for any sign of shock or stress for the next day or so.

Every system will be different, but you may want to get into the habit of cleaning your system every month or so until you can determine an ideal schedule to clean your hydroponic system. You may also opt to clean your hydroponic system in between plant growth cycles.

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