How To Decontaminate A Hot Tub: The Step-By-Step Line Flush Protocol That Pros Actually Use 

By Mike Ruff — Owner, Daytona's Best Pool Service. CPO® & PHTA Certified. Licensed and Insured.

If you Google "how to decontaminate a hot tub," you'll get a hundred articles that say roughly the same thing: "drain your tub every few months, add a line flush product, and fill it back up." None of them tell you exactly what product, in what amount, with the jets running how long, in what sequence, with what to do if you see the gunk shoot out, and how to rebalance the chemistry afterward.

That's why most hot tub owners either skip decontamination entirely or do it wrong. Both end up the same place: biofilm in the plumbing, sanitizer that won't hold, mysterious smells, and a $400 service call six months later.

I've been doing pool and spa decontamination work for over seven years. I'm a CPO® through the Pool & Hot Tub Alliance, fully licensed and insured. The protocol below is what I actually run on customer tubs — step by step, with the exact amounts, sequencing, and recovery procedures. Read all of it before you start. Set aside about 3-4 hours of mostly hands-off time. And follow the order — skipping steps is what stalls most decontaminations.

Before You Start: What This Process Will Do

A proper line flush physically dislodges the biofilm that has formed on the inside of your hot tub plumbing. Biofilm is a slimy bacterial layer — invisible from your tub water but living in every length of pipe between your pumps and your jets. It protects bacteria from your sanitizer, which is why your bromine or chlorine keeps "disappearing" no matter how much you add.

When the line flush works correctly, you'll see something most owners aren't prepared for: visible gunk blasting out of the jets. Black flakes. Brown streamers. Slimy gray ribbons. Sometimes in volumes that look impossible coming out of a tub that "looked clean."

That stuff was living inside your plumbing. It's coming out, finally, where you can drain it.

This is normal. This is the point.

What You'll Need

Get all of this before you start. Stopping mid-process to drive to the store is how decontaminations get botched.

A line flush product. Brand recommendations: Ahh-Some is the gold standard ($30-35, a small tub lasts multiple uses). Oh Yuk Hot Tub Cleaner, Spa System Flush, and Spa Marvel Cleanse all work well too. Don't substitute generic dishwasher detergent or homemade mixes — they lack the surfactants needed to actually break the biofilm matrix.

A drain hose long enough to reach an appropriate disposal site (more on that in Step 4) and a sump pump or submersible utility pump if your tub doesn't have fast-drain.

A wet/dry shop vac for cleaning the empty footwell.

A spa surface cleaner (non-abrasive, vinyl- and acrylic-safe).

A fresh filter cartridge if yours is over 6 months old. Otherwise, filter cleaner solution for an overnight soak.

A garden hose plus, ideally, a hose-end pre-filter if you have hard or metal-heavy fill water.

A real test kit. Test strips can't read what you need to know at the levels you'll be working in during a fresh fill. I use the Taylor K-2006 on every service call. The pH, alkalinity, calcium hardness, and sanitizer readings during the rebalance step all matter, and they need to be accurate.

Chemical-resistant gloves and safety glasses. Non-negotiable.

Fresh chemicals for the refill: sodium bromide and bromine tabs (or dichlor for a chlorine system), pH up and pH down, alkalinity increaser, calcium hardness increaser.

Step 1 — Add The Line Flush To Your Existing Dirty Water

Counter-intuitive but correct. You're going to drain this water anyway. Adding the line flush product to dirty water lets the product do its work while you don't waste a fresh fill on the process.

Remove your filter cartridge entirely and set it aside. The line flush will dislodge biofilm that would otherwise immediately clog and contaminate the filter — and if your cartridge is over 6 months old, you'll be discarding it at the end of this process anyway.

Add the line flush product per the label instructions. For most brands, this is roughly 1-2 tablespoons per 350-400 gallons. Don't overdose — more isn't better here; more just creates more foam during the flush phase.

Step 2 — Run All Jets At Full Power For 30-60 Minutes

Turn the tub to its normal operating temperature. Turn on every jet bank. Open all the air control valves. Run the spa with the cover on if you can — this lets the product circulate without massive evaporation and contains the foam.

About 10-15 minutes in, foam will start to rise. By 20-30 minutes, you'll start seeing visible debris in the water — sometimes black, sometimes brown, sometimes a kind of gray-green that looks like watery sludge.

Let it run.

If the foam threatens to overflow the cover seal, briefly turn off jet banks one at a time to manage it. Don't add defoamer — that would interfere with the line flush product's surfactant action.

At the 45-60 minute mark, the volume of new debris coming out should be tapering off. Some lines need a second cycle to fully purge; for a tub that's never been decontaminated, plan on the full 60 minutes minimum.

Step 3 — Shut Down And Prepare To Drain

Turn the tub off at the breaker. Yes, the breaker — not just at the panel. Working on a hot tub with live 240V circuits is a real electrocution hazard, and you don't need power during a drain.

Open the cover and let any remaining foam settle. Skim out any solid debris that's floating on the surface with a net so it doesn't get sucked into your drain hose.

Step 4 — Drain The Tub

Connect your drain hose to the tub's drain port (or position a submersible pump in the footwell).

Where the water goes matters. This water is now full of biofilm fragments, dead bacteria, sanitizer residue, and line flush surfactant. It is not appropriate to drain into:

A vegetable garden, lawn, or anywhere plants you eat from would absorb it.

A septic system or septic drain field. The surfactant load alone can disrupt septic bacteria.

A storm drain. In most jurisdictions this is technically illegal.

A pool or pond.

It is appropriate to drain into a sanitary sewer cleanout (the kind plumbers use to access your home drain system), a graveled or paved drainage area that flows to a municipal storm system through proper filtration, or — depending on local rules — a non-edible landscape area at least 50 feet from any water body. If you're unsure, the safest option is to drain into your sanitary sewer through a basement floor drain or via a hose run into an indoor drain.

Plan on 1-3 hours to fully drain a 400-gallon tub depending on hose diameter and gravity.

Step 5 — Clean The Empty Tub

Now you can see what you couldn't see before. The empty tub will likely have a fine sediment layer in the footwell — vacuum it out with your shop vac. The waterline ring will be more visible — wipe it down with the spa surface cleaner.

Pay special attention to:

The footwell, especially around the suction drain covers. This is where settled biofilm fragments end up.

The jets themselves, particularly the rotary jets that have removable nozzles. Some can be pulled out and soaked in vinegar to dissolve scale and biofilm.

The headrest pillows. They absorb body oils and harbor bacteria. Remove them if possible and wash separately with mild soap.

The skimmer / filter housing.

Don't use household cleaners. Don't use abrasive scrub pads. Don't use bleach directly on an acrylic shell. Spa surface cleaners are formulated to be safe on the materials your tub is made of — household products can permanently dull or damage the finish.

Step 6 — Rinse-Fill (Optional But Strongly Recommended)

This is the step most YouTube tutorials skip, and it's the difference between a good decontamination and a great one.

Fill the empty tub with cold water just to about 12 inches deep. Briefly turn the breaker back on, run the jets for about 10 minutes (water level must be over the jets), then shut down and drain again. This catches any remaining line flush product and any final biofilm fragments that were dislodged from the deepest plumbing runs.

You'll often see another wave of debris during the rinse-fill — usually smaller and lighter than the first round, but real. That's biofilm from plumbing the original flush didn't quite reach.

After the rinse-fill drain, wipe down the footwell one more time and you're ready for the real refill.

If you're working with limited time, you can skip this step — but every spa tech I respect does the rinse-fill on stubborn tubs, and it cuts down on "weird foam" issues during the first week back in service.

Step 7 — Refill With Fresh Water

Fill the tub through the filter cartridge slot (or through a skimmer with the filter removed). This slows the fill but eliminates airlocks in the plumbing — air pockets that would otherwise cause your pumps to run dry on first startup and potentially burn out the shaft seals.

If you have hard fill water or you're filling from a well with metals, use a hose-end pre-filter during the fill. They're $30-50 and they prevent calcium and metal staining issues from day one.

Fill until the waterline reaches the manufacturer's "fill line" — typically about an inch above the highest jet. Insert a fresh filter cartridge once you're at the fill line.

Step 8 — Power Back On And Begin Chemistry

Turn the breaker back on. Let the tub begin heating to operating temperature (this takes 4-12 hours depending on your heater). The pumps should be running normally during heating.

While the tub is heating, test your fill water. You'll get a baseline that helps you understand what your fill water is doing to your chemistry over time. Write the numbers down.

Once the tub reaches operating temperature, balance in this exact order:

First, alkalinity. Target 80-120 ppm. Add baking soda if low; add small doses of dry acid if high. Alkalinity is the buffer that keeps pH from bouncing — fix it first, and the rest of the chemistry stabilizes.

Second, pH. Target 7.4-7.6 for chlorine systems, 7.4-7.8 for bromine systems. Use pH down (dry acid) to lower, pH up (sodium carbonate) to raise.

Third, calcium hardness. Target 150-250 ppm. Add calcium chloride if low. If your fill water tests above 250, you don't have a direct way to lower it short of dilution — make a note for next time and possibly add a sequestrant.

Fourth, sanitizer. For a bromine system, add your sodium bromide bank per the product label (typically 1.5-2 oz for a 400-gallon tub on fresh fill) and place fresh bromine tablets in the floater. For a chlorine system, dose granular dichlor to bring free chlorine to 3-5 ppm.

Run the jets for 15-20 minutes after each chemical addition. Then re-test before adding more. The number-one cause of post-fill chemistry problems is overdosing — chemicals take time to dissolve and circulate, and panicking before they've had time is how you end up at the opposite end of the range you're trying to hit.

Step 9 — Let It Cycle For 24 Hours Before Use

This is non-negotiable. Even with a perfect balance, fresh-fill water needs at least 24 hours to fully equilibrate and for the sanitizer to establish itself throughout the plumbing — the same plumbing you just decontaminated. Resist the urge to soak immediately.

Test again at the 24-hour mark. Adjust as needed. If everything is in range, you're ready.

What Comes Next: Don't Let It Get Bad Again

A successful decontamination resets your tub to "new." But biofilm starts forming again the moment fresh water hits warm plumbing. The discipline that keeps it from re-establishing is built into the maintenance routine, not the recovery routine. That means:

Decontaminate every 90 days. Not "next time it gets bad." Every 90 days, treated as non-negotiable. Set a recurring calendar reminder. This is the single most important habit a hot tub owner can build, and it's the one most owners skip until they're calling a pro.

Never let sanitizer hit zero. Test before every use. Test twice a week even when you don't soak. The window when sanitizer is at zero is the window when biofilm gets a foothold.

Keep the filter clean. Rinse weekly. Deep-clean monthly. Replace yearly. A clogged filter recirculates contamination instead of removing it.

The complete weekly maintenance routine, the dosing chart for every chemical adjustment in a 400-gallon spa, the troubleshooting flowcharts for foam/cloudy/smell/skin reactions, and the printable 90-day maintenance calendar are all in The Hot Tub & Spa Owner's Maintenance Guide for $19.97. The decontamination protocol you just read is from Chapter 5 of the guide — written more compactly in the PDF, with the dosing tables and quick reference pages laid out for printing and lamination.

A Few Things That Go Wrong (And How To Handle Them)

Foam keeps coming back during the flush. Normal. Don't add defoamer mid-process. Briefly cycle jet banks off to manage volume.

Almost no debris comes out during the flush. Either your tub is genuinely clean (rare on a first-ever decontamination) or your product dose was too low. Run a second cycle with a fresh dose of line flush.

The pump won't prime after refill. Air lock. Most pump unions have a small bleed screw — loosen it briefly until water comes out steadily, then re-tighten with the pump running. If you can't find or operate the bleed screw, call a pro before running the pump dry for more than a couple minutes.

Sanitizer still won't hold a week after a "successful" decontamination. Possible causes: biofilm too established for a single home flush to fully resolve (run the full protocol a second time, two weeks later), filter not actually replaced when it should have been, or there's an undetected pump or plumbing issue. If two consecutive decontaminations don't restore normal sanitizer hold, call a spa pro — there may be a deeper plumbing problem.

Cloudy water 48 hours after refill. Usually means alkalinity or pH wasn't balanced before sanitizer was added. Test, adjust, run the jets for an hour, retest. Should clear within 24 hours.

When To Call A Pro

Most hot tub owners can decontaminate their own tub successfully — I've walked dozens of homeowners through this exact protocol over the phone. But there are situations where calling a licensed pool & spa pro is the smarter call:

If your tub is still under warranty, check before doing anything that involves running chemicals through the plumbing aggressively. Some manufacturers consider line flush products acceptable; others get sticky about anything beyond their recommended cleaners. Better safe than facing a warranty denial.

If you have any electrical issues, error codes, or signs of pump or heater failure, address those first with a pro. Decontaminating won't fix broken equipment, and you don't want to discover a leak only after you've refilled.

If you've decontaminated twice and the problem persists, you may have biofilm in a configuration home flushes can't reach (typically inside heaters or in unusually long plumbing runs in luxury spas). A pro can do aggressive purges with stronger industrial chemistry and specialized circulation tools.

If you're in the Daytona Beach / Port Orange / New Smyrna FL area, that's literally what we do. Daytona's Best Pool Service offers hot tub decontamination, equipment repair, and quarterly maintenance plans. Reach out through the site if you want it handled.

For everyone else: you've got this. The protocol works. The investment is a couple of hours and about $30 in product. The payoff is months of trouble-free soaking, sanitizer that holds the way it's supposed to, and a hot tub that lasts the 15+ years it was built to last.

Get the complete Hot Tub & Spa Maintenance Guide for $19.97 →

Twenty-eight pages, written by a working CPO. The decontamination protocol above is one chapter — the rest covers weekly maintenance, troubleshooting, equipment care, dosing charts, and a printable 90-day calendar.

And before you start: get a real test kit. The chemistry rebalance step depends on accurate readings, and strips can't deliver them at the precision a hot tub needs.

— Mike Ruff Owner, Daytona's Best Pool Service CPO® & PHTA Certified · Licensed and Insured