How to Flush a Tankless Water Heater (90-Min Annual Descale)

How to flush a tankless water heater, the 90-minute annual descale

A tankless heat exchanger that's never been descaled at year 5 is a $1,200 replacement waiting for the right Tuesday. Mineral scale builds inside the exchanger, restricts flow, raises pressures, and eventually pinholes a brazed joint. Most homeowners never know it's a maintenance item, it's not on any manufacturer's "set up" checklist they read once and lost. Below: the 90-minute annual descale, the gear ($50-$90 one-time), and the half-step that wrecks heat exchangers when people skip it.

✓ Field Verified Reviewed by Al, the Building Doctor (IUOE Local 39 · 30-Yr Pro) · Credentials & Standards →

Tankless water heater isolation valves and service ports

Annual 90-Minute Vinegar Descale & Heat Exchanger Flush · Field Procedure Field Verified

Annual minimum. Every 6 months on hard water (15+ GPG).

Rinnai, Navien, Rheem warranty terms commonly require documented descaling. Skip it and a warranty claim for a clogged heat exchanger is on you. Write the descale date on a piece of tape stuck to the unit cover.

Gear you need

Submersible pump + hose kit ($50-$90): Eccotemp EZ-Flush, Calci-Clean, or generic. One-time buy, lasts forever. Don't try to skip this.
5-gallon bucket (clean, no detergent residue).
Two 3/4" washing-machine hoses, usually come with the pump kit.
4 gallons white vinegar (5% acetic acid, grocery store) OR CLR Pro Calcium Lime Rust Remover (1 gal concentrate diluted per label). Vinegar = non-toxic, gentler, 60 min. CLR = stronger, 45 min, more careful disposal.

The 7-step procedure

Power off + gas off. Shut off the unit switch or breaker. Shut off the gas valve. Wait 15 minutes for the heat exchanger to cool.
Shut off water + isolate. Close the hot-side and cold-side isolation (service) valves, handles labeled HOT/COLD. Open the small drain ports on each service valve over a bucket to relieve pressure.
Connect hoses. One hose: from the cold-side drain port to the submersible pump (inside the bucket). Second hose: from the hot-side drain port back into the bucket. Now you have a closed loop.
Fill with descaler. Pour 4 gallons of vinegar (or CLR per label) into the bucket. Open both service-valve drain ports.
Run the pump 45-60 min. Descaler circulates through the heat exchanger and back to the bucket. You'll see scale chunks accumulate in the bucket, that's the goal. On hard water, the bucket will look like the bottom of a coffee pot.
Flush with fresh water, the half-step nobody skips. Turn off the pump. Dump the descaler bucket. Disconnect the pump return hose. Open the cold-side isolation valve briefly to flush fresh water through the heat exchanger and out the hot-side hose into the bucket. Run for 5 minutes. Vinegar/CLR residue left in the exchanger eats brass fittings and feeds biofilm, flush thoroughly.
Reconnect + restore. Close service-valve drain ports. Disconnect hoses. Open both isolation valves. Restore gas, then power. Run a hot-water tap for 30 seconds to confirm flow + temperature.

Also do this while you're in there, clean the inlet filter screen

Cold-side has a small filter screen behind a cap near the cold isolation valve. Unscrew the cap, pull the screen, soak in vinegar 5 minutes, rinse, reinstall. Scale and pipe debris accumulate here and restrict flow, most "low hot-water pressure" complaints I take on tankless units trace to this $0 fix.

Vinegar vs CLR, which one

Factor	White Vinegar	CLR Pro
Strength	Mild (5% acetic acid)	Strong
Time required	60 min	45 min
Safe for stainless heat exchangers	Yes	Yes (per CLR Pro spec sheet)
Safe for copper heat exchangers	Yes	Yes (but flush thoroughly)
Disposal	Drain (it's vinegar)	Per label / household chemical disposal
Cost (annual descale)	$12 (4 gal grocery store)	$25 (1 gal concentrate)
Best for	Soft water, mild scale	Hard water (15+ GPG), thick scale

Brand-specific notes

Rinnai (RX, RU, RXP series): isolation valves with built-in drain ports are standard on units sold post-2018. If your install is older, you may need to add isolation-valve kits ($80) before you can descale.
Navien (NPE, NPN): built-in maintenance kits standard. Same procedure. Some models display a maintenance reminder on the panel after 1,500 hours of runtime.
Rheem (RTGH): isolation valve kit usually included with new installs. Check for hot/cold labels: Rheem's are sometimes reversed compared to Rinnai conventions.
Bosch (Greentherm), A.O. Smith, Stiebel Eltron Mini: same general procedure, but verify your specific service-valve port location in the manual before connecting.

FAQ

Vinegar or CLR?

Both work. Vinegar is non-toxic, gentler, 60 min. CLR stronger, 45 min, more disposal care. Hard water (15+ GPG): CLR. Soft water: vinegar.

How often do I descale?

Annual minimum. Every 6 months on hard water (15+ GPG). Warranty terms often require it.

Can I descale without a pump kit?

Not effectively. Static fill doesn't circulate. Pump kit is $50-$90 one-time.

Will descaling fix low hot-water pressure?

Sometimes. Also clean the inlet filter screen (cold side, under cap near isolation valve), most common cause of low flow.

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Editorial standards: Procedure verified against Rinnai, Navien, Rheem service manuals. Reviewed by Al, Building Doctor, IUOE Local 39 Stationary Engineer.