We’ve got some bad news…the most important part of running a hydroponic garden that is sustainable long-term is deep cleaning. That’s right, every gardener’s favourite pastime. Fortunately for you, a thorough cleaning will reduce your garden’s risk of pests and diseases, and increase the size of your harvest. Plus, it’s easier than you think. Let’s dive in. 

In today’s newsletter, we will take you through our step-by-step cleaning process, covering the different kinds of systems and growing media. Before we do, you must understand why cleaning your system is essential.

Aside from the obvious, a dirty system is an ugly system; there are lots of benefits to maintaining a clean growing area: 

👉🏼 It makes your life easier. A clean system makes all your other processes more manageable. It’s easier to spot pests and diseases quickly. It’s easier to harvest. It’s easier to replant. 

👉🏼 It reduces the risk of pests and pathogens carrying over from one harvest to the next. 

👉🏼 It means your plants uptake 100% of the nutrients you give them – no need to share with neighbouring algae growth.

Before you get started cleaning, you’ll need a few things: 

✅ Rubber gloves

✅ Sponge or scrubber 

✅ A bucket

✅ A water source 

✅ Bleach or hydrogen peroxide

The first step is to clear out your system. 


If you’re growing in coconut coir, you’ll want to dump out your growing media as well as any spent plants, roots and foliage. Coco Coir is organic and excellent at retaining water, so if you don’t want it to go to waste, add it straight into the garden as a soil improver. 


If you’re growing in perlite, you can reuse your media a couple of times before it must be discarded. 

As your perlite ages, you’ll notice green algae growing on top. This algae is unsightly, but it does not affect how your system operates – you can mix it through your system if it’s bothering you. 

When your perlite begins to turn from crisp white to murky grey/green, you know it’s time to wash or replace your media. If you plan to replace your perlite, discard your existing media entirely. 

If you plan to reuse your perlite, you’ll need to pick out any plant/root matter (gently shaking your pot should help debris move to the top) before rinsing the whole lot. 

We dump ours in a wheelbarrow and cover it in a solution of 1:5 hydrogen peroxide (50%) to water, which soaks for 10 minutes. Once soaked, we spread the perlite on a tarp and let it air dry. Perlite is super lightweight, so drying it out needs to happen undercover, or the wind will blow your media away. 

Once the perlite is dry, it’s ready to use again. 


Like perlite, expanded clay will accumulate mineral (salt) buildup and algae growth over time. Neither mineral nor algae build-up will cause problems for your system (within reason), but this kind of growth can be off-putting. 

To clean and reuse your expanded clay, you’ll need to remove spent plants and plant matter from the media. We use a blower vac on the lowest setting, which makes this job a breeze.

Remember, good expanded clay can be washed and reused indefinitely while low quality expanded clay will break down over time. We recommend investing in Liaflor German expanded clay, which is what we have been using for the last 35+ years. 

Once again, after you’ve removed any debris, you’ll want to rinse your media in that same hydrogen peroxide solution before air drying and reusing it in your system. 

Now you’ve emptied your system and cleaned your grow media, it’s time to deep clean.

Start by taking your system apart. Empty out the water in your reservoir, remove plumbing and separate system components.

Soak all your small parts, such as joiners, elbows and tees, end caps, tubing and drippers, in a bucket of water and hydrogen peroxide. 

While that’s happening, soak your cloth in that bucket and wipe all your system components down one at a time. Take care to wipe down the inside and outside of your system. Even when the outside of your system looks clean, it can be the perfect environment for harbouring bugs or pathogens waiting to wreak havoc on your new crop. 

Now, it’s time to assemble your system. Put everything back together, checking the openings of your plumbing and fittings for blockages. 

Once everything is back together, add your washed media and plant a new crop. 

If you’re ready to clean your hydroponic system, we’d recommend using Oxy Plus, a 50% hydrogen peroxide solution from Growth Technology. We’ll include a link to this product below. 

That’s all we have for this month’s newsletter. If you have any questions about cleaning your media or system, call our friendly team at 1800 640 222. Until next time, happy growing!