Cleaning Your Vertical Hydroponic Tower: Step-by-Step Guide

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While the allure of hydroponics often lies in the thrill of cultivating diverse plants, fine-tuning your growing strategies, and relishing the fruits of your labor, cleaning is an indispensable aspect that shouldn’t be overlooked.

Though it might lack the excitement of harvesting, a well-maintained hydroponic system is key to achieving long-term success and bountiful yields.

Keeping your hydroponic tower clean is easy with just water, white vinegar, and elbow grease. Regular cleaning, from scrubbing away algae to sterilizing components, will ensure optimal plant health and yields.

This article will offer a step-by-step guide to routine cleanings, along with tips for an annual deep clean. Let’s get started and give your tower the TLC it deserves.

My hydroponic tower is in need of a good clean!

First, why does cleanliness matter?

A dirty system can become a breeding ground for harmful bacteria, mold, and algae, which not only compromise plant health but can also clog your system’s tubing and pumps.

These contaminants can interfere with nutrient uptake and oxygen availability, ultimately leading to weaker plants, stunted growth, and increased susceptibility to disease.

In short, a clean system is a functional system, vital for optimal plant growth and yield.

How often should you clean your hydroponic tower?

Both routine and annual cleanings are crucial for the longevity and productivity of your hydroponic tower.

Weekly and monthly cleaning

Maintaining a clean hydroponic tower year-round is essential for optimal plant growth. This involves proactive measures such as promptly addressing any signs of contamination within the system.

Top tip: Read my articles on how to prevent and remove algae in your hydroponics system.

I recommend disassembling the tower for a comprehensive cleaning every few months to ensure it remains in peak condition. This article will demonstrate one such cleaning using a 5% vinegar solution.

Annual cleaning

I advise conducting a thorough cleaning and sterilization of your hydroponic tower annually.

Sterilization eliminates harmful bacteria that may be hiding in your system, bacteria that can cause root diseases and adversely affect plant growth and yield.

For this purpose, you can use high-quality bleach that is deemed food-safe.

What cleaning agents can you use?

Here are some cleaning agents that are generally considered safe and effective for hydroponic systems:

Hydrogen Peroxide (H2O2)

This is a great option for cleaning and disinfecting your hydroponic system. It breaks down into water and oxygen, leaving no toxic residues. There are plenty of good, food-grade solutions on Amazon.


If used in low concentrations and thoroughly rinsed afterward, food-safe bleach can be an effective sterilizer.

White vinegar

Effective for cleaning but needs to be thoroughly rinsed to prevent any acidity from affecting the nutrient solution. Not as effective as bleach or hydrogen peroxide for sterilization.

Cleaning your hydroponic tower: Step-by-Step Guide

In the following sections, I’ll walk you through the step-by-step process for cleaning your hydroponic tower system.

While this serves as a general blueprint, remember that your system might have its own specific needs. Nonetheless, the core cleaning principles should be universally applicable.

Step 1: Disassemble the tower

A. Unplug electrical components

Start by unplugging all electrical components connected to your hydroponic tower, such as water pumps and grow lights, and automatic plug timers to eliminate any safety hazards.

Top tip: It’s best to clean your tower outside if you’re able as it can get quite messy.

B. Plant removal

Once you’ve done that, carefully remove your plants and their respective growth mediums from their holders and set aside safely. If you’re currently not growing anything you can disregard this step.

If (like me) you haven’t properly removed dead and dying plants from a previous grow cycle – now is a good time! Dispose of them safely and turn them into compost.

Dead tomato plants left over after harvest

C. Disassembly

Now you’re ready to disassemble the main parts of the tower: the trays, water reservoir, tubes, and any other modular sections your system may have. Make sure you don’t lose any small components.

Step 2: Drain, remove debris and rinse

A. Drain the reservoir

After disassembling the tower, the next step is to drain any remaining water from the reservoir and tubes. To do this, carefully drain the old nutrient solution either down the drain or use it as fertilizer for other plants.

B. Clear away debris

You’ll want to clear out any noticeable debris, such as fallen leaves or root matter, from all components. Use a soft brush or cloth to gently scrub away any stubborn particles.

Make sure to get right into the vertical tower itself and remove any debris from the inside. This can be quite disgusting so feel free to wear gloves if you’re squeamish!

Lots of rotten roots from my old tomato plants

C. Rinse

Once all debris is cleared, thoroughly rinse each section with clean water. Make sure to rinse the reservoir, trays, and tubing to eliminate any leftover nutrient solution or deposits.

This prepares all parts of your tower for the more targeted cleaning and sterilization (which is only needed for deeper annual cleans) steps that follow.

Step 3: Mix your cleaning solution

A. Mix white vinegar and warm water

For this routine cleaning, we’re going to use a simple yet effective solution made from white vinegar and warm water. In a large bucket or bowl, mix one part white vinegar to four parts warm water.

Stir the solution well to ensure it’s thoroughly blended.

This solution will help to dissolve mineral buildup and kill off mild bacteria and mold, setting the stage for a more detailed cleaning process.

Top tip: If you are planning on doing a deeper clean (For example, between growing cycles or before you stop using your tower), you can use a food-safe bleach solution.

Step 4: Scrub all components clean

Now that your cleaning solution is ready, it’s time for the fun part.

A. Soak components in the vinegar solution

Immerse each disassembled component of the hydroponic tower into the vinegar and warm water mixture for about 20 minutes before attempting to scrub them.

B. Scrub down the compontnets

Using a non-abrasive scrub brush, thoroughly scrub all surfaces of the trays, reservoir, tubes, and any other sections you’ve taken apart.

Pay particular attention to corners and crevices where debris and bacteria are more likely to accumulate.

Remember, the goal is to remove all traces of mineral buildup, algae, and other potential contaminants.

C. Scrub down the tower itself

That includes all of the components AND the main structure of the vertical hydroponic tower itself (inside and out). The tower can be a little tricky to clean, though.

Do your best to get inside the tower and behind all the crevices. This is much easier if your tower is modular.

3D-printed towers or those made from a single piece of PVC tubing like mine are harder to clean as they generally don’t come apart.

Step 5: Rise everything off

A. Rinse with water to remove traces of the vinegar or bleach solution

After you’ve thoroughly scrubbed all the components, it’s crucial to rinse off any remaining cleaning solution to prevent residue that could harm your plants.

Use clean water to rinse each part of the tower—trays, reservoir, tubes, and any other disassembled elements. Make sure you rinse thoroughly to eliminate all traces of the vinegar solution.

A powerful hose can be used to clean the inside of your tower

Top tip: If, like me, you are not able to get to the inside of your hydroponic tower to clean it, then you can use a power washer or a powerful garden hose to clear as much debris and contaminants as possible.

A good rinse ensures that your hydroponic system is not only clean but also free of any chemicals that could interfere with your plants’ growth or nutrient uptake.

Step 6: Leave to dry

Once rinsed, set the components aside on a clean surface or towel to air dry before reassembling your tower.

Step 7: Reassemble

Once all components are clean and have fully air-dried, you can start the reassembly process.

Refer to your tower’s assembly instructions as needed, and remember to reconnect any electrical components like water pumps and grow lights once your tower is back in position.

Double-check all connections and fittings to ensure they are secure; you don’t want any leaks once the system is operational again.

Finally, plug in the electrical components and run a quick system test to make sure everything is working as it should.

Step 8: Refill and restart

A. Refill the reservoir

Now it’s time to refill the water reservoir and restart your system. Add fresh water to the reservoir, and don’t forget to include your nutrient solution, following the manufacturer’s instructions for ratios and measurements.

Top tip: You can read my step-by-step guide to changing the nutrient solution in a hydroponic system for more information.

Once the water and nutrients are in place, restart the water pump and any other electrical components you have, like grow lights or fans.

B. Restart your tower

Once the water and nutrients are in place, restart the water pump and any other electrical components you have, like grow lights or fans.

C. Perform one last system check

Perform a final check to ensure there are no leaks and that all components are functioning correctly. Observe the water flow and nutrient distribution to confirm everything is running smoothly.

Once you’ve verified that all systems are go, you can reintroduce your plants to their freshly cleaned environment, or start planting new ones.

Step 9: Re-start growing

Congratulations! You’ve successfully cleaned and restarted your hydroponic tower, setting the stage for optimal plant growth and yield in the coming weeks.

Remember, it’s always a good idea to clean little and often, with one deeper annual clean with bleach to sanitize the system.

Tips for maintaining your vertical hydroponics tower

Regular maintenance goes a long way to prevent common problems from occurring and, ensuring the longevity of your hydroponic tower and optimizing plant yields.

Make it a habit to visually inspect your system weekly for signs of mold, algae, or mechanical issues. Perform smaller cleanings every few weeks and don’t skimp on the annual deep clean!

Top tip: For a comprehensive guide to keeping your tower in peak condition year-round, refer to my “Ultimate Guide to Hydroponic Tower Maintenance.

Keep in mind the ‘checklist’ above when thinking about how to maintain your tower.

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William, an experienced consultant and passionate advocate for technology and sustainability, is the founder of Smarter Home Gardens. William's journey into gardening began with the purchase of his first home, which came with a small backyard garden. Despite initial challenges brought about by limited space, soil, and sunlight, William's determination to create a vibrant garden led him to research and experiment with innovative gardening technologies and sustainable practices. Driven by his lifelong enthusiasm for technology and sustainability, William explored various gardening methods, including vertical gardening, hydroponics, companion gardening, and composting. Through these efforts, he realized that it was possible to combine his passions with his newfound love for gardening. Smarter Home Gardens was born out of William's desire to share his research and experiences with others, helping them create smarter gardens that leverage cutting-edge technology and contribute to a more nature-positive world. The blog offers in-depth articles on innovative gardening technologies and methods, helpful 'how-to' guides, reviews of the latest gardening technology, and research on cost-effective garden maintenance solutions. William's commitment to sustainable and technologically-driven gardening has made him a trusted voice in the field. His enthusiasm for creating gardens that work with the planet, rather than against it, is evident in every post he shares on Smarter Home Gardens. Through the blog, William hopes to engage with a wider audience, encouraging others to join him on this exciting journey towards smarter, more sustainable gardens.

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