How to Sanitize Your RO System and Clean the Storage Tank
Your RO water tastes a little off. Maybe there's a faint musty smell, or the system sat unused while you were away. The fix is almost always the same thing: sanitize the storage tank.
There are two kinds of RO tanks, and they need different procedures. Atmospheric tanks (the big open-air kind on whole-house RO) get drained, scrubbed, and refilled with bleach solution. Bladder tanks (the small pressurized ones under your sink) get sanitized through the plumbing without ever being opened. Both are below.
Key Takeaways
When to Sanitize
Atmospheric Tank
Bladder Tank
Bleach Type
Bladder tank: Small (3 to 4 gallons), sealed, pressurized, lives under your kitchen sink as part of a point-of-use RO system. You can hear water enter when you open the RO faucet. Sanitize through the plumbing, never open it.
Atmospheric tank: Large (165 to 1,000+ gallons), open to the air at the top, sits in a basement, garage, or utility room as part of a whole-house RO system. Usually paired with a delivery pump. Drain, scrub the interior, refill with bleach solution, then flush.
When to Clean Your RO Tank (and Safety First)
Storage tanks are where bacteria love to settle. They hold filtered water at room temperature for hours or days, and the membrane upstream has already stripped the chlorine that would normally keep things sterile.
- Once a year as routine maintenance, even if the water still tastes fine
- After any repair that opens the system to outside air (filter changes, membrane swaps, fitting work)
- After 2+ weeks of disuse (a vacation, second home, seasonal property)
- Immediately if you notice musty smells, off-tasting water, cloudiness, or visible sediment
This guide is for sanitizing your tank, not for drinking. The bleach ratios below are for cleaning the tank and plumbing only. Always flush the system completely after sanitizing, then use chlorine test strips to confirm 0 ppm free chlorine at the faucet before drinking. If there's any doubt, don't drink the water. Call a licensed water treatment professional.
Handling bleach. Wear gloves and safety goggles. Work in a ventilated space. Never mix bleach with ammonia or other cleaners. Drain rinse water away from gardens, lawns, and septic systems (chlorinated water harms plants and beneficial bacteria). Don't enter a large atmospheric tank unless you have confined-space safety training, the right equipment, and a spotter.
About these ratios. Dosages here follow published shock-chlorination practice for potable water storage. The 50 to 100 ppm free chlorine range targeted by the 2 cups per 100 gallons formula is consistent with Oregon Health Authority shock-chlorination guidance, which references ANSI/AWWA C652 (the industry standard for disinfection of water storage facilities). When your system manufacturer's instructions say something different, follow theirs.
How to Clean an Atmospheric RO Storage Tank
Atmospheric tanks (commonly 165, 220, or 500 gallons on residential whole-house setups) are open to the air at the top, so sediment settles at the bottom and biofilm builds on the interior walls. It's more involved than a bladder tank, but it's an afternoon plus an overnight soak. Crystal Quest's atmospheric tank lineup covers the common residential and light-commercial sizes.
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Shut down and drain.
Turn off water to the tank and the RO system. Power down any delivery pumps. Open the drain valve and let the tank empty. A wet/dry vacuum or sump pump pulls out anything left at the bottom.
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Remove debris.
Vacuum out any sediment, biofilm flakes, or scale. This is the step most people skip, and it's the one that matters most. Debris harbors bacteria that survive a chlorine soak. The more you physically remove now, the better the disinfection works.
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Scrub the interior (if your tank has an inspection port).
Use a long-handled brush or pressure washer. Hit the corners, seams, and the area around fittings, where biofilm tends to build. Rinse and vacuum out the rinse water. No access port? Skip ahead. The bleach soak handles it.
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Disinfect with bleach.
Add 2 cups (16 oz) of unscented household bleach per 100 gallons of tank volume, then refill with clean water. Use the dosage card below for common sizes. Open downstream valves periodically so chlorinated water circulates through the connected plumbing too. Let it sit for at least 6 hours, ideally overnight.
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Flush and rinse.
Drain the chlorinated water away from any landscaping or septic system. Refill with clean water and drain again. Repeat at least twice, or until you can't smell chlorine anymore. Test strips are a fast, inexpensive way to confirm you've hit zero ppm before reconnecting.
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Reconnect and restart.
Reconnect the plumbing, restart the RO system, and run one or two full cycles before drinking. Run the kitchen and bathroom taps too, so you flush chlorine out of the rest of the house's plumbing.
The standard rate is 2 cups of unscented household bleach (5 to 6% sodium hypochlorite) per 100 gallons of tank volume. That puts the soak solution at roughly 50 to 100 ppm free chlorine, which matches ANSI/AWWA C652 (the industry standard for water tank disinfection) and CDC tank-sanitization guidance.
| Tank Size | Bleach Amount |
|---|---|
| 165 gallon | 3.3 cups (26 oz) |
| 220 gallon | 4.4 cups (35 oz) |
| 500 gallon | 11 cups (88 oz) |
Unscented only. Scented or "splashless" bleach contains additives that shouldn't go anywhere near a drinking water system. See the safety notes above before starting, and remember to flush to 0 ppm chlorine before drinking.
How to Clean a Bladder (Under-Sink) RO Tank
Bladder tanks are sealed pressure vessels with a flexible diaphragm separating the water from a compressed air charge (7 to 10 psi when empty). You never open them. Sanitizing happens by circulating bleach solution through the plumbing, letting it sit, and flushing it out. About an hour of work plus a short soak.
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Shut down and depressurize.
Turn off the water supply valve to the RO system. Open the dedicated RO faucet and leave it open until water stops flowing. Tank needs to be fully empty and depressurized before you start.
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Remove the filters and membrane.
Pull the pre-filters (sediment, carbon), the RO membrane, and the post-carbon filter. Bleach destroys these, so they have to come out before sanitizer enters the system. Set them on a clean towel in the order they came out so reinstallation is straightforward.
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Add the sanitizing solution.
Mix 1 to 2 teaspoons of unscented household bleach into 1 gallon of clean water. Pour it into the empty pre-filter housing using a funnel. That's how you get sanitizer into the tank without ever cracking it open. (An NSF/ANSI 60 listed potable-water sanitizer works the same way if you'd rather skip bleach.)
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Circulate and soak.
Reattach the empty filter housings (no filters or membrane installed yet). Turn the water supply on briefly, just long enough to push the sanitizer into the tank. Shut it off. Let everything soak for 15 to 30 minutes. If your tank is small enough to move, gently rock it to coat the bladder evenly.
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Flush thoroughly.
Open the RO faucet and drain the tank completely. Refill, drain again. Repeat 2 to 3 times until there's no chlorine smell. The final drain should taste and smell like nothing at all.
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Reinstall and restart.
Put the filters and membrane back in the right positions, watching membrane orientation (there's usually a flow arrow). Turn the system on, check every fitting for leaks, let the tank fill once, and discard that first tank as a final precaution.
Once a week or so, drain the bladder tank fully. Open the RO faucet and let it run until empty. Fresh water refills throughout the day. Simple habit, less standing-water time, longer interval between deep cleanings.
Atmospheric vs Bladder: Quick Reference
| Atmospheric Tank | Bladder Tank | |
|---|---|---|
| Capacity | 165 to 1,000+ gallons | 3 to 4 gallons |
| System type | Whole-house RO | Under-sink (point-of-use) RO |
| Pressure | Open to atmosphere (delivery pump required) | Sealed and pressurized (7 to 10 psi empty) |
| Bleach ratio | 2 cups per 100 gallons | 1 to 2 tsp per gallon |
| Soak time | 6+ hours (overnight) | 15 to 30 minutes |
| Interior access | Through inspection port (scrub interior) | None (sanitize through plumbing only) |
| Total time | Half day plus overnight soak | About 1 hour active |
Troubleshooting Common Tank Issues
| What You're Seeing | Likely Cause | What to Do |
|---|---|---|
| Musty or swampy odor | Bacterial growth or biofilm in the tank | Sanitize using the procedure above |
| Low water flow at the faucet | Bladder tank air pressure is low | Check pressure with the tank empty, adjust to 7 to 10 psi |
| Tank won't fill, or fills slowly | Ruptured bladder, faulty check valve, or fouled membrane | Replace the tank or check valve, or service the membrane |
| Cloudy or milky water | Air in the system, or a bacterial bloom | Flush thoroughly. Sanitize if it doesn't clear within a day |
If sanitizing doesn't fix a recurring smell or taste issue, the problem's usually upstream. A fouled membrane or saturated post-carbon filter passes through compounds the tank cleaning won't address. See how to replace your RO filters, clean an RO membrane, or replace an RO membrane if any of those are overdue. The complete RO maintenance guide ties it all into one annual schedule.
Need a replacement tank or sanitization supplies?
Crystal Quest's storage tanks, replacement filters, and water specialists are here when you need them.
FAQs About Sanitizing Your RO System
How often should I sanitize my RO system?
Once a year for both atmospheric and bladder tanks. Sooner if the system has been unused for more than two weeks, after any repair that opens the system to outside air, or any time you notice a change in taste or smell.
Can I sanitize my RO system without removing the membrane?
No. Sodium hypochlorite damages thin-film composite RO membranes (the kind in nearly every residential system) on contact, and it's not reversible. Always remove the membrane before introducing bleach, then reinstall it after the final flush. Atmospheric tank cleanings happen upstream of the membrane in most whole-house configurations, but verify your specific layout first.
Is bleach safe to use in a drinking water system?
Yes, when you use the right kind and flush thoroughly. Unscented household bleach (5 to 6% sodium hypochlorite, no additives) is the same active ingredient municipalities use to disinfect tap water. The key is rinsing until no chlorine residual remains. NSF/ANSI 60 listed sanitizers work too if you'd rather not use bleach.
Why does my RO water smell bad even after cleaning the tank?
If sanitizing doesn't fix it, the issue's upstream of the tank. A saturated post-carbon filter is the most common culprit (it stops adsorbing odors as it nears end-of-life), followed by a fouled or expired RO membrane. Replace the post-carbon filter first; if the smell persists, service the membrane.
Do I need to sanitize the tank if I just changed all the filters?
It's the right time to do it. The system's already partially open, the membrane's out (or about to be), and you're going to flush the lines anyway. Sanitizing during a filter change adds maybe 30 minutes for a bladder tank or part of an afternoon for an atmospheric tank, and saves you a separate teardown later.
Can I use vinegar instead of bleach to clean an RO tank?
Vinegar dissolves mineral scale, but it doesn't disinfect at the level a drinking water tank needs. It won't kill the bacteria or biofilm that are the actual reason you sanitize. Stick with unscented bleach or an NSF/ANSI 60 listed sanitizer for the disinfection step. A vinegar rinse beforehand is fine if your tank has visible scale buildup.
