How to Clean & Sanitize a Reverse Osmosis System

Written by: James Smith

Updated: April 10, 2023

A reverse osmosis system offers clean, filtered water in the home but you’ll need to look after it carefully. We’ve got an easy guide which explains how to clean your RO system in simple steps.

Sanitizing RO system

Everyone knows the health benefits of drinking water but there’s something even better about enjoying a drink of filtered or bottled water.

Rather than spending lots of money on buying plastic bottles at the supermarket, a reverse osmosis system in your own home can achieve a similar result.

However, to keep on enjoying the same high-quality water, you’ll need to carry out some reverse osmosis system maintenance from time to time.

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If you’re not technically-minded the idea might fill you with horror, but the good news is that it’s not quite as tricky as it sounds.

We’re here to help you through the process with our step-by-step guide to cleaning and sanitizing your reverse osmosis system, including how to spot when it’s time to carry out the work.

Ready? Time to roll up those sleeves and get started…

Why Your Reverse Osmosis System Needs Cleaning

One of the benefits of using a filter is that you can enjoy water that’s free of harmful bacteria.

However, over time, micro-organisms can build up within the system and lead to the accumulation of biofilm. If you don’t sanitize and clean your system regularly, the water produced could be contaminated.

Water filter with dirty water

Cleaning your system isn’t just about making sure you’re getting the quality of water that you want, it also protects the system too. If you don’t carry out regular cleaning and maintenance, there’s a risk that your system could be damaged by the build-up of potentially harmful biofilm.

Cleaning your reverse osmosis system doesn’t have to be difficult but it will keep your system working properly and producing the quality of water you expect.

Why Carry Out Reverse Osmosis Maintenance?

Your filter and membrane will need to be changed at specified intervals so it’s easier to carry out the cleaning at the same time. The instruction manual for your particular model will confirm how often these changes need to take place. But generally speaking, a membrane will last a year and the filters 3-6 months.

3 used water filters

However, if the water system in your home is subject to a critical event, such as a flood or a hurricane, it is a good idea to carry out a complete clean before using your reverse osmosis system again.

This is because the domestic water supply is usually compromised during these kinds of disasters and chemicals can be pushed into the system.  This can put your system under enormous pressure and flood it with contaminants.

To be sure that your system hasn’t been compromised or stressed beyond its capability, it’s recommended to carry out a complete clean and sanitization before use.

Recommended Reading: Don’t miss our guide to the top performing whole home RO systems.

How to Sanitize Your RO System

We’ll start with a list of things you’ll need before we get onto the steps to take.


Your shopping list

Step-by-step process

If you want to know how to sanitize your reverse osmosis system, we’ve broken it down into a step-by-step guide to walk you through the whole process.

  1. Make sure the area you’re going to be working in is free of dust and as clean as possible
  2. Get the filters, and membrane if applicable, ready but don’t open them just yet.
  3. Switch off the water supply that is connected to your reverse osmosis (RO) system.
  4. If the system is hooked up to your refrigerator, make sure you disconnect this too.
  5. Wash your hands and put on the eye protection and gloves.
  6. Open the RO faucet and allow the whole system to drain.
  7. Once the drainage is complete, close the faucet.
  8. Remove the pre-filter first. This is the first filter that the water has to pass through. To do this you’ll need to open the housing and take out the old filter first.
  9. Do the same for all of the filters before the tank, but don’t touch the post-filter just yet.
  10. Remove the membrane and set to one side.
  11. Don’t put the new filters in but close the housing and screw back into position.
  12. Pour the sanitizer into the pre-filter housing. Unscented bleach can also be used.
  13. Switch the water back on and allow the system to refill.
  14. Once full, check for any leaks. This process could take 10-15 minutes.
  15. Check to see if the system is fully operational by turning on the RO faucet. If water comes out as normal, switch the faucet back off and turn the incoming water supply off again
  16. You’ll now need to leave the sanitizer in situ for as long as it takes to work. Check the pack for the individual timings. If you’re using unscented bleach, 30 minutes should suffice.
  17. Once the time is up, open up the faucet and allow the RO system to fully drain.
  18. You’ll need to flush the system through to allow the cleaner to be properly rinsed away. Do this by opening up the water supply for about five minutes, closing it and then turning on the faucet to let the system drain. You’ll need to repeat this at least twice.
  19. If you can still detect an unusual smell, repeat the flushing until the water smells normal
  20. Close off the water supply once more.
  21. Open up all the housings, unpack the new filters and put them in place.
  22. Switch the water on and check for any leaks
  23. Once your tank has refilled, you will now have a fully sanitized system and purified water of the highest quality.
  24. If you disconnected your refrigerator, don’t forget to hook it back up!

The above steps explain how to sanitize your RO system but if you also need to clean up your membranes, there’s a little more work to do.


How to Clean the Reverse Osmosis Membrane

If you can change your RO filters, you’ll find reverse osmosis membrane cleaning just as easy! Here’s another step-by-step guide on how to get the job done:

  1. Follow the same process as sanitization up to step number 7
  2. Disconnect and remove the membrane from the RO housing.
  3. Follow the instructions on the chemical cleaner. It’s important that you purchase a product designed for use in RO systems (see the shopping list section above).
  4. There are usually several steps to the cleaning process and they must be followed in the correct order. Typically this means an acid then alkali clean, followed by a sanitizer with the membrane flushed between each.
  5. As well as cleaning the membrane, take this opportunity to also clean the housing using simple dish detergent and a bottle cleaner
  6. Dispose of all chemicals
  7. Rinse the housing and membrane thoroughly
  8. Re-assemble the parts and place back into the RO system
  9. Switch on the water supply and check for leaks
  10. Flush the system through several times (as described in steps 18-19 above)

You may find it takes a few hours for the water quality to return to normal.

Recommended: We explain how to remineralize RO water.

How Long do Reverse Osmosis Filters Last?

The length of time you should leave between changing your RO filters really depends on the individual manufacturer. Check your RO system manual for guidance on how often they recommend changing the filter.

However, as a general guide reverse osmosis filters normally need to be changed every 3-6 months and membranes every 1-2 years.

You should change your filters at the recommended intervals even if the water looks perfectly fine. This is because there may be degradation taking place which is not visible to the eye.

There are some signs that you can look out for that indicate you should change your filter, even if it’s not due just yet. These include:

  • Water that tastes funny. If you notice a weird aftertaste in your drinking water, it’s a definite sign to change your filter. A quick sanitization and filter change should resolve the issue
  • Low water pressure. Filters that are due a change are one possible cause for low pressure. Changing the filters could solve the problem but if not, you’ll need to look for an underlying issue with the system itself
  • Taking a long time to fill a glass of water. This is usually just due to an overloaded filter; once changed it should revert back to normal speed.

You should also consider whether your membrane needs cleaning too as this can produce similar problems to a filter that’s due for a change.

Enjoy Top Quality Water

Having a reverse osmosis system offers many benefits but to continue enjoying the very best quality water, you’ll need to clean, replace and sanitize the system periodically. Allow 2-3 hours for the whole process from start to finish, and don’t be tempted to skip any steps to speed things up!

Sanitizing your system and flushing your RO membrane isn’t difficult and once you’ve been through the process, you might be surprised at how simple the maintenance really is.

About the Author James Smith

James is the chief water geek here at His mission is to empower the consumer and allow people to take control of their health. His passion for water health is contagious, hopefully unlike your tap water!

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