Clean and Sanitize your AeroGarden for Hydroponic growing

This post follows our research editorial guidelines.

Brock Ingham
Brock Ingham

AeroGarden is technically considered a closed-loop system. Despite this, they will still need a good cleaning every so often. This will ensure that you don’t accidentally play host to some harmful bacteria that could make you incredibly sick.

Cleaning your AeroGarden regularly will also improve the longevity of your water pump system. Follow these foolproof steps for a safe long-lasting AeroGarden experience.

Clean and Sanitize your Aerogarden for Hydroponic growing

When should you be cleaning your AeroGarden?

It’s recommended to clean your AeroGarden after each full harvest. If your not sure when a harvest is complete look for the plants that are no longer producing flowers or fruit. This is a sign that dormancy has begun which is a perfect time to remove and clear your system.

If you are growing lettuce or leafy vegetables in your AeroGarden, then look for flowers beginning to appear. This means your plant is “bolting” and will try to produce seeds. Lettuce and greens that have gone to seed create a bitter taste to ensure the seeds have a chance to germinate. These leaves are not something you want to add to your dinner plate so go ahead and discard the plant entirely.

The other way you can clean your AeroGarden is when the plants are still being grown. Sometimes dirt, fallen leaves, or other debris may fall into the top of your growing tray. This can be quite annoying especially if you have a white model like the original AeroGarden Harvest. In this case, simply wipe the top of the growing tray with a damp paper towel or lightly vacuum any dry fallen debris. Be sure to not use any harsh chemical cleaners or soap during a mid-grow clean as they might harm your plants.

We recommend that when you sanitize your AeroGarden to only use safe cleaners like bleach or distilled white vinegar. While bleach may seem harsh it’s similar to chlorine found in tap water. Unlike some bio-based cleaners, bleach won’t leave behind a chemical residue when rinsed. When in doubt, trust the tried and true! If you feel uneasy about using bleach try distilled vinegar. The worst-case scenario, you might have some funky smelling dressing on your hands.

Step 1: Start by removing your pods and drain the tank

It goes without saying, you can’t fully clean your AeroGarden while your plants are still growing.

So, the first thing is first. Remove your used seed pods, scrape out the growing medium, and set aside the empty pods.

Remember, with a bit of time and finesse you can re-use these seed pods to reduce your growing costs. Once your seedpods have been removed gently rinse out the water reservoir and seed tray.

Step 2: Prepare your water reservoir

Start by filling up your now empty water reservoir with water 1/3 of the height that you would normally fill. This will avoid any damaged parts from the concentration of cleaner. Diluting your cleaner in the water solution first will prevent the cleaner from splashing up in your face.

Step 3: Prepare your sanitizer mixture

If you are looking to run a deep cleanse on your AeroGarden system,

then be sure to use bleach during this process. To make the cleaning mixture combine ¼ cup or 4 tablespoons of bleach with the already 1/3 filled water that is now sitting in your water reservoir. If you are using vinegar instead of bleach then increase the concentration to 4 cups of vinegar.

Step 4: Run the pump

Now that the water reservoir is full of the water/sanitizer solution it’s time to turn on the pump. Sit back and relax for 5-7 minutes while the cleaning solution rids your system of harmful bacteria.

Step 5: Rinse

Once the 5-7-minute pump cycle is complete, you may go ahead and dump the cleaning solution. Give your AeroGarden a good rinse with warm water. Re-fill your water reservoir with room temperature water, free of any cleaning solution.

Step 6: Make sure to run the pump with water only

Now that you have run a full sanitizing cycle and rinsed the machine thoroughly it’s time to repeat the pump cycle, this time only using water that is free from cleaners. Fill the tank with water only and run the pump again for 5-7 minutes. If the pump is not cleaned from a run of only water, residual cleaner may be left behind. It’s an important step to follow that will keep your pump running like new!

Step 7: Drain the water reservoir

You’re almost there! Once the water pump cycle has run its full 5-7-minute course you are ready to dump the water and rinse again. This time use cold water to avoid excessive condensation.

Step 8: Allow time to dry

Give your AeroGarden system a break and let it dry out for 48 hours. Once this time has passed you are ready to get back to growing.

Optional: How to clean your AeroGarden pods

To re-use your seed pods they will need to be thoroughly sanitized. This is especially important if you plan to grow the same variety of vegetables or herb in the pod used before.

Step 1: Remove plant and growing medium

Before you start, remove the plant from the pod that has been harvested, either save for later or discard it entirely. Carefully scoop out the grow sponge which is acting as the growing medium of choice.

Step 2: Rinse the empty pods

Now that there is only a small amount of growing medium left on the pod, you can go ahead and rinse off what remains. Peat moss is a slow to break down growing medium which could cause havoc on your plumbing system if not properly removed before rinsed.

Step 3: Soak in a cleaning solution

Refer to the mixing instructions described above to get a safe solution for you to use. Since you will not be using the water reservoir as a measuring cup you can simply find a large bowl. Fill the bowl with 1/3 water then mix in either ¼ cup of bleach or 2 cups of vinegar. Fill up the rest of the bowl with water until about 2 inches from the top of the bowl. Place your rinsed pods in the bowl and let them soak for 12 hours.

Step 4: Rinse and dry

drying on a towel

Once the soaking is complete, rinse the pods thoroughly with warm water for 1-2 minutes. Set them each aside on a clean towel to dry. Once dry they will be ready to fill back up with an unused pack of peat moss or a clean grow sponge for the next planted seed.


Having bacteria grow in your AeroGarden system can dismantle your ecosystem over time. A system that is not cleaned on a regular basis makes for a great home to the harmful bacteria. These pathogens will attack your plants’ root systems hindering their ability to absorb nutrients. If nutrients can not be absorbed then you can expect stunted growth. Once these pathogens strike it’s often too late to recover. If damage like this is suspected it’s best to start over again after a deep clean to avoid the transfer of disease to future crops.

Good Garden Tip

To avoid causing damage to your plants. You should wash your hand thoroughly during the growth phase. This is especially important before pruning or harvesting your crop. Similarly, any garden tools like sheers or scissors should be sanitized before use to avoid infection.

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