How to Sanitize a Reverse Osmosis System

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There’s no denying that a reverse osmosis system is one of the best investments for anyone who’s concerned about their home’s drinking water quality.

This water filtration solution is one of the most effective available, removing more than 99.9% of all total dissolved solids, making water clean, pure and safe to drink.

But an RO system won’t maintain this high quality of performance without a little help from you. Aside from changing the filters as recommended by the manufacturer, you should also sanitize the system to prevent recontamination and ensure it can function at its peak.

Considering your main reason for purchasing a reverse osmosis system was probably to enjoy clean drinking water, you want to make sure you can keep it that way.

In this guide, I’ll be sharing a step-by-step process on how to sanitize reverse osmosis system. I’ll also share how to clean your reverse osmosis membrane and how to clean out your RO tank.

1️⃣ How to Sanitize a Reverse Osmosis System

Most manufacturers will recommend that you sanitize your reverse osmosis system on a once-yearly basis.

If, like me, you struggle to keep track of time, I would advise marking a year from now in your calendar and making a note to clean your system. You could also choose to sanitize your system when you change your sediment and carbon filters, which typically have a lifespan of 12 months to 1 year.

The two most suitable sanitizers for reverse osmosis systems are Sani-System Sanitizer, an NSF-approved non-bleach product, or unscented bleach.

Pro Products SANI-SYSTEM

Follow the steps below to sanitize your reverse osmosis system with your pick of these products.

❗️ Before beginning, I highly recommend checking your system’s manual. It will include detailed instructions about any specifics for cleaning your unit. You will also need to replace the post-filter after this process, unless it removed & bypassed.

1. Wash & Prepare

Before getting started, wash your hands with soap and hot water. For extra protection, put on a pair of cleaning gloves. Make sure the area you’ll be cleaning your system in is as clean as possible. Wipe away any lingering dust before you get started.

2. Turn Off Your Water

Turn off the water supply underneath your kitchen sink. For systems connected to icemakers or refrigerators, close the line to prevent water from being able to travel into these appliances.

How to Sanitize a RO System - Step 2 Turn Off Your Water

3. Drain Your Tank

Open the RO faucet, allowing for all the water to drain out of the system’s storage tank. Drain the system fully before closing the faucet again.

How to Sanitize a RO System - Step 3 Drain Your Tank

4. Remove the Pre-Filter

Open the housing that stores the pre-filter (this will usually be closest to the ingoing feed line that connects to the left side of the system). Remove the filter from the pre-filter housing. If you’re replacing the filter after sanitizing your system, discard it as recommended by the manufacturer.

How to Sanitize a RO System - Step 4 Remove the Pre-Filter

5. Remove the Remaining Filters

Remove the rest of the filters from the filter housings in the filtration system, including the reverse osmosis membrane. Again, if you’re installing new filters, you can throw out (or recycle) your old filters. If any of your filters don’t need replacing yet, place them on a clean, sterile surface for the time being.

How to Sanitize a RO System - Step 5 Remove the Remaining Filters

6. Re-attach the Filter Housing

Attach the filter housings back to the filtration system, apart from the pre-filter housing. Remove the pre-filter housing if you haven’t already. Don’t add any filters to the filter housing yet.

How to Sanitize a RO System - Step 6 Re-attach the Filter Housing

7. Add Your Cleaner

Add unscented bleach or Sani-System sanitizer to the pre-filter housing and attach it back onto your reverse osmosis system.

How to Sanitize a RO System - Step 7 Add Your Cleaner

8. Fill the System

Turn on your cold water supply. This will flush the system with the sanitizer solution. It should only take up to 10 minutes for the system to fill without the filters or RO membrane installed. Make sure there aren’t any leaks during this process. If there are, turn off your cold water supply and hand-tighten your fittings.

How to Sanitize a RO System - Step 8 Fill the System

9. Flush & Repeat

Open the RO faucet and wait until water flows out, which indicates that the water has made it all the way through the RO system. Turn off the water faucet and leave the system for up to 30 minutes. If you’re using Sani System, you’ll only need to wait for 1 minute.

How to Sanitize a RO System - Step 9 Flush & Repeat

10. Drain & Refill the System

Once this time has passed, turn the RO faucet back on and wait 5 minutes, until the water no longer smells of bleach. Turn off the cold water supply line and let the system completely drain. Repeat this twice, turning on the feed water, allowing the system to fill, turning on the faucet, turning off the feed water supply, emptying the system, and so on.

How to Sanitize a RO System - Step 10 Drain & Refill the System

11. Finishing Touches

After this, you’ll be ready to use the RO system again. Replace the filters with new filters, or put the old ones back into their housing. Turn on the cold water supply and check for leaks as the system fills. With the filters in place, it’ll take several hours for the storage tank to fill.

How to Sanitize a RO System - Step 11 Finishing Touches

2️⃣ How to Clean a Reverse Osmosis Membrane

It’s not just the filter housing of reverse osmosis systems that needs an occasional clean. You can benefit hugely from cleaning out the RO membrane, especially if your filter’s performance has started to flag in recent months.

Of course, you should only clean your RO membrane as recommended by your manufacturer, and not as an alternative to buying a new one. When it’s time for a replacement, no amount of cleaning will improve the membrane’s filtering abilities. It’s important to replace RO membranes as advised by the manufacturer, even if your water still looks and smells clean.

The easiest way to clean the RO membrane is to prepare a cleansing bath. Follow the instructions below to give your membrane a new lease of life:

1. Gather Your Materials

There are several materials you’ll need to clean your RO membrane, including a plastic bucket, rubber gloves, and cleaning chemicals designed for the job (there are a number of RO membrane cleaners you can buy online for the best results). You may also want to wear protective eyewear for this process.

How to Clean a RO Membrane - Step 1 Gather Your Materials

2. Remove the Membrane

Shut off your water supply and remove the membrane from its housing in the RO system. Set the membrane on a clean, sanitized surface and put the membrane housing to the side for now.

How to Clean a RO Membrane - Step 2 Remove the Membrane

3. Prepare a Cleaning Solution

Fill a plastic tub with water and the recommended quantity of chemical cleaner. There are a number of different cleaning solutions that can be used to remove limescale, oil, grease, mildew, mold, and so on. Only mix cleaners if you’re certain that it’s safe to do so. Otherwise, you should repeat the following process, using a different cleaner each time.

How to Clean a RO Membrane - Step 3 Prepare a Cleaning Solution

4. Soak the Membrane

Place the membrane inside the cleaning solution, making sure it’s fully submerged under the water. Leave it to soak for an hour (or a time specified by the manufacturing company of the cleaning chemical). Once the time has passed, take the membrane out of the cleaning solution and rinse thoroughly under your faucet for 5 minutes.

How to Clean a RO Membrane - Step 4 Soak the Membrane

5. Return the Membrane to the System

Put the membrane back inside the housing and connect the housing to your RO system. Turn on the water supply and open your RO faucet. Let water flow out of the faucet for up to 30 minutes, which will flush out the chemicals and ensure your water is safe to drink from.

How to Clean a RO Membrane - Step 5 Return the Membrane to the System

3️⃣ How to Clean a Reverse Osmosis Tank

Finally, the storage tank in an RO system is a potential breeding spot for all sorts of germs, making it perhaps the most important component to clean regularly. The more contaminated water becomes while in storage, the more work the post-filter will have to do, too, and you’ll likely have to change this water filter on a more frequent basis.

If you followed the procedure for sanitizing your RO system, you will have already cleaned out the tank and post-filter. But if you just want to clean the storage tank on its own, follow the steps below:

❗️ You will also need to replace the post-filter after this process, unless it removed & bypassed.

1. Shut Off Your Water

Shut off your cold water supply and open the RO faucet to relieve water pressure from inside the system.

How to Clean a RO Tank - Step 1 Shut Off Your Water

2. Remove the Tank

Close the tank valve, then remove the tank from the RO system, bringing the connecting tube with it. If there’s still any water in the tube, drain it now.

How to Clean a RO Tank - Step 2 Remove the Tank

3. Add Your Cleaner

Add a little unscented bleach (around half a teaspoon) to the inside of the tube, then carefully reconnect the tube to the RO system, making sure the bleach doesn’t spill out.

How to Clean a RO Tank - Step 3 Add Your Cleaner

4. Fill the Tank

Open the tank valve, then turn on your water supply, allowing time for the tank to fill with water. Check for leaks during this process. Make sure your tap is switched off.

How to Clean a RO Tank - Step 4 Fill the Tank

5. Leave For 30 Mins

When the tank is full, let the bleach sit for at least 30 minutes, which will allow it to kill any microorganisms, like bacteria, that could be inside the tank. After this time is up, you can open your tap and drain the system.

How to Clean a RO Tank - Step 5 Leave For 30 Mins

6. Refill & Repeat

Let the tank refill for a second time, then repeat the process, draining the water out of your faucet. Repeat the cycle for a final time if you can still smell the sanitizer.

How to Clean a RO Tank - Step 6 Refill & Repeat

❔ Frequently Asked Questions

Do I really need to clean my reverse osmosis system?

Yes. Cleaning RO systems with a sanitizer doesn’t only prevent the growth of bacteria; it also means that you’ll have access to the highest quality filtered water constantly (as long as you also replace your pre-filters or post-filter regularly). Cleaning can also protect your RO unit and help it to live the longest life possible, enabling you to get more out of your investment.

It’s a good idea to follow the system cleaning process as advised by your manufacturing company, along with any other suggested maintenance, such as replacing your old filter cartridges with new filter cartridges.

How do I know when my reverse osmosis system needs cleaning?

You might notice something obvious, like a bad smell coming from your tank. Your water may also taste funny, suggesting that some contaminants aren’t being filtered out.

But oftentimes, you won’t know when your water filtration system needs to be cleaned out. You may also confuse signs that your filters need changing with signs that your system needs sanitizing. That’s why I would suggest noting in your calendar to clean your water filter once every 12 months or as recommended by the manufacturing company.

What if cleaning my system doesn’t help?

If you sanitize your RO system and find it still smells bad or looks past its best, it may be time for a new filter system entirely. If they’re properly looked after, most reverse osmosis filter systems last for 10 to 15 years. Some parts may wear out before this time, and you may find that it’s less hassle to replace your system with an updated model.

How do I clean a countertop reverse osmosis system?

It’s usually much simpler to clean a countertop reverse osmosis system because the filters are contained within a small, compact unit that isn’t connected to your water line. Again, you will need to run bleach or a specialized cleaning product through the system (with empty housings – remove the filters first), waiting until the storage tank is filled with water before emptying it out and refilling/emptying the system several times over until your water no longer smells of bleach.

Which cleaners are safe to use for sanitizing my RO filters?

Your user manual should have some information about the best cleaners to use for sanitizing your system, but you could contact the seller directly for clarification. I would strongly recommend that you don’t simply use one of the household cleaners you have in your cleaning cupboard.

My advice would be to either purchase a specially designed RO sanitizing solution or make your own out of white vinegar and water. You need to sanitize the system without contaminating it with something that may linger in the system even after flushing it several times.

  • Michael Claybourn
    Water Treatment Specialist

    With 25+ years in water treatment, Michael Claybourn Sr. (WT Specialist 3) leads his company, Water of Texas LLC, in solving industrial, commercial, and residential water challenges. From filtration to ozone, he tackles any task, from initial consultation to equipment maintenance. His passion, honed in nuclear power and Culligan of Brazosport, fuels his commitment to delivering pure, healthy water for every client.

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