Cleaning a reverse osmosis system means sanitizing the housings, tubing and storage tank, and it is done at a filter change because that is the only time everything is open. The one rule that matters is what comes out first: chlorine based sanitizer destroys the membrane permanently, so the membrane and any carbon cartridges are removed before anything is introduced.
Shut down and strip out
Close the feed valve and the tank valve, then open the RO faucet and leave it open until pressure is released and flow stops. Drain the storage tank through the faucet, which takes a while and is worth doing properly, since a tank half full of old water defeats the point. Remove all the cartridges and, critically, the membrane, keeping the membrane somewhere clean and wet if it is being reused. Carbon cartridges also come out, because carbon will simply adsorb the sanitizer and neutralise it.
Sanitize the empty system
Follow the manufacturer's method and dose, which is usually a measured amount of unscented household bleach or a proprietary sanitizer introduced into the first housing. Reassemble the empty housings, open the feed slowly, and let the solution fill the system and the storage tank. Then close the feed and leave it to stand for the contact time the manufacturer gives. Open a few taps of solution through the RO faucet during that period so the tubing and the faucet itself are treated rather than only the housings.
Flush until it is genuinely gone
Drain the tank completely, then refill and drain it again, repeating until there is no smell of sanitizer at all. This takes longer than people expect and it is the step most often cut short. Only then fit the new cartridges and the membrane, in the correct order and the right way round. Run the commissioning flush the manual specifies for new media, which is normally at least two full tank fills, before anyone drinks from it.
How often, and what it does not fix
Once a year, at the annual filter change, is the usual interval, and more often if the system has stood unused for a long period or if there has been a boil notice. Sanitizing addresses biological growth in the housings, tubing and tank. It does not restore a spent membrane, clear a blocked prefilter or fix a tank that has lost its air charge, all of which produce symptoms people hope a clean will cure. Our whole house RO guide covers the same discipline at larger scale.
Questions people ask about how to clean a reverse osmosis system
Can I sanitize with the membrane still in place?
No. Chlorine based sanitizer destroys the membrane permanently. Remove the membrane and any carbon cartridges first.
How often should an RO system be sanitized?
Annually, at the filter change, and additionally after a long period of disuse or a boil water notice.
How do I know the sanitizer is flushed out?
Fill and drain the tank repeatedly until there is no smell at all, then run the commissioning flush for the new cartridges on top of that.
Will cleaning improve slow production?
Rarely. Slow production is usually a blocked prefilter, low line pressure or a tank that has lost its air charge, none of which sanitizing addresses.