RO System Sanitization
Updated February 20, 2026
Reverse osmosis systems produce incredibly clean water, but the moist, dark environment inside the filter housings is also a perfect breeding ground for bacteria. Every time you change filters, you should sanitize the system. Skip this step and you can end up drinking water that's been filtered through a bacterial colony -- defeating the whole purpose of having an RO system.
Overview
Reverse osmosis systems produce incredibly clean water, but the moist, dark environment inside the filter housings is also a perfect breeding ground for bacteria. Every time you change filters, you should sanitize the system. Skip this step and you can end up drinking water that's been filtered through a bacterial colony -- defeating the whole purpose of having an RO system.
What to Know
Step by Step
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Shut off the water supply and tank valve
Close the feed water valve to the RO system. Close the valve on the storage tank (the blue valve on the tank line). Open the RO faucet to depressurize the system and drain any remaining water.
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Remove all filters and membrane
Using the filter wrench, unscrew each housing and remove the old filters. Remove the RO membrane from its housing. Set the membrane aside if you're reusing it (it doesn't go back in until after sanitizing).
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Add sanitizer
Pour 2-3 tablespoons of unscented bleach into the first (sediment) filter housing. Screw the empty housings back on -- no filters installed. Make sure the membrane housing is reconnected but empty.
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Fill the system with sanitized water
Turn the feed water back on. Open the tank valve. Let the system fill completely -- water will pass through all empty housings and tubing, carrying the bleach solution. Let the tank fill. Then open the RO faucet and run until you smell bleach -- this confirms sanitized water has reached every part of the system.
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Contact time and drain
Close the faucet and let the sanitized water sit in the system for 30 minutes. Then open the faucet and drain the entire tank. This may take 15-30 minutes. Close the tank valve and feed water.
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Install new filters and flush
Install all new pre-filters, the membrane (new or reused), and the post-filter. Open the feed water and tank valve. Let the tank fill completely, then drain it through the faucet. Repeat one more time. The water should have no bleach taste or smell after two full tank flushes.
Pro Tips
- Take a photo of the filter arrangement before disassembling. RO systems have a specific filter order that matters.
- The filter wrench that came with the system is essential. Keep it near the system -- trying to unscrew housings by hand usually doesn't work.
- If you notice a biofilm (slimy coating) on removed filters, the system is overdue for sanitization.
- Date-label each new filter at installation so you know exactly when it went in.
Mistakes to Avoid
- Skipping sanitization during filter changes -- the most common RO maintenance mistake.
- Using scented bleach or bleach with additives -- these leave residues and tastes.
- Not flushing enough after sanitizing -- two full tank cycles minimum.
- Installing filters in the wrong order. Pre-filter stages are numbered for a reason.
When to Call a Pro
If the system has persistent taste or odor issues after sanitization and fresh filters, the tank bladder may be contaminated and need replacement. If you're uncomfortable working with the system, a water treatment specialist can service it in about an hour.
Bottom Line
Sanitize every time you change filters. Bleach, 30 minutes of contact time, two full flushes. It takes 45 minutes total and keeps your RO system producing clean, safe water instead of breeding bacteria in the dark.