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How to Treat a Well, Step by Step

Last updated Reviewed by Sean Mihelich, founder of Save My Well

Treating a well with a disinfectant is also called shock chlorination. Treating a well means putting enough disinfectant into the water column to kill the bacteria living in the well, the pressure tank, and the pipes, then flushing it out and proving it worked. Here is the whole job, both ways to do it, and where people go wrong.

Transcript

Can you shock a well yourself? First, know the five moments when your well needs a test. One is a flood, so do not drink the water yet, and call a well contractor. Two is a new pump or any repair, because the well was opened up. Three is a test that shows coliform germs in the water. Four is a new smell or color, since that can mean your water changed. Five is digging or building work close to your well. In the other four, test first, then shock if germs show up. Follow the Save My Well DIY kit, and keep the hose loop that stirs the well. After the shock, test again in a week or two. If germs still show up, call a licensed well contractor. Get the Save My Well DIY kit at save my well dot com.

Voice: Kyutai TTS 1.6B by Kyutai (CC BY 4.0), voice "developer-1" (CC0).

Step 1: find out how much water your well holds

Every treatment starts with the same number: gallons of standing water. A borehole holds 0.0408 × diameter² gallons per vertical foot, so a 6-inch well with 100 feet of standing water holds about 150 gallons. You need the well's depth, its diameter, and the static water level. Most states recorded all three when the well was drilled, and we can pull your official well record from your address in seconds.

Step 2: pick your disinfectant

The traditional method is chlorine: plain unscented 5.25% bleach or calcium hypochlorite pellets, dosed to reach 50 to 200 ppm of free chlorine per the university extension guides (see Minnesota Department of Health). It kills bacteria, and it is what most contractors reach for. Per EPA's disinfectant guidance, chlorine is less effective as pH rises, and most well water sits above pH 7. It also reacts with dissolved iron before it reaches bacteria, and at that strength it is corrosive to a pump and fixtures.

The newer method is chlorine dioxide, the disinfectant many municipal water plants use. Our kit ships it as sealed Selectrocide pouches that generate 99.9% pure chlorine dioxide in water, dosed at 20 ppm following the manufacturer's published guidance. EPA's guidance notes that chlorine dioxide stays in its molecular form across the pH of natural waters, and its maker publishes data that it penetrates biofilm. We wrote up the full comparison in chlorine dioxide vs bleach.

Skip the math. We will size your treatment dosage for you.

Answer a few questions about your well. The kit is from $329, with a lidded mixing pail and a bacteria test before and after. For context, a professional treatment visit can cost up to $500, and it may not include a bacteria test.

Look up my well See what's in the kit

Step 3: run the treatment

Either way, start by bypassing your water softener and any filters. With bleach, the extension guides dose the well to 50 to 200 ppm and hold it 12 to 24 hours.

With our treatment kit, follow the Selectrocide label. Make a 500 ppm stock first: open each package without cutting the envelope, throw away the desiccant, and submerge the envelope in the lidded mixing pail from the kit, in 10 liters of water for a 5G or 24 liters for a 12G, one pouch at a time, with the lid closed. Wait at least 2 hours, then take the envelope out and mix gently. Work in a well-ventilated area, wear gloves if your hands will touch the solution, and wear a NIOSH-approved respirator for chlorine dioxide if you work with the stock in an open container.

Pour the amount of stock your plan lists into the well. The label then says to circulate the solution through the lines with the system's pump: run a garden hose from an outside spigot back into the well so the pump moves the solution through it, then close the cap. Run about 6 ounces through every faucet and shower, and let the solution stand overnight, about 12 hours, with no water use.

Step 4: flush, then prove it worked

The next day, flush the solution through every faucet and outlet, and flush the well from an outside spigot onto ground that drains away from your septic system, your garden, and any surface water. Then retest for bacteria one to two weeks later. A treatment without a follow-up test is a guess. Our kit includes both bacteria tests, and your plan email carries each step with your well's own numbers.

How to disinfect a well

Disinfecting a well, sanitizing a well, and chlorinating a well are names for the steps above. The CDC (May 2025) gives the same outline after a flood or other emergency: put disinfectant in the well, run it to every faucet, leave it in the well and plumbing for at least 12 hours, flush, and wait at least 7 to 10 days before testing. Fix any opening at the wellhead first, or the bacteria come right back.

How to sanitize a well

Sanitizing is the word on many store-bought packs, and the job is the same: size the dose to the gallons of water in the well, circulate it, hold it, flush it, and retest. The size is the step most people skip. A well holds its depth below the water level times the gallons per foot for its casing, which step 1 explains, and our guide to finding your well depth helps when there is no record.

How to chlorinate a well

Chlorinating means using a chlorine product, such as unscented bleach or calcium hypochlorite. Penn State Extension (updated May 2025) calls it a fix for one-time contamination and says a well whose bacteria keep returning needs a continuous disinfection system. Ohio State Extension (June 2019) says to let the chlorinated water stand in the pipes 12 to 24 hours and retest about two weeks later. Our kit does the same job with chlorine dioxide pouches. For what to use when one treatment is not enough, see our well water treatment guide, and for an E. coli result, our E. coli guide.

Need the numbers for your own well? The well disinfection calculator gives the gallons, the bleach amount, and the kit for it.

Straight answers

How much bleach does it take to treat a well?

It depends entirely on how much water your well holds. Extension services publish targets of 50 to 200 ppm of free chlorine, and a borehole holds 0.0408 times its diameter in inches squared, in gallons per vertical foot of water. A typical 6-inch well with 100 feet of standing water holds about 150 gallons. Guessing is how people end up with a well that still tests positive, or a week of bleach coming out of every tap.

How long after treating a well can I drink the water?

Give the treatment its full contact time: overnight, about 12 hours, for the chlorine dioxide in our kit, as its label directs, and 12 to 24 hours for a bleach treatment per extension guidance. Then flush the treated water out through every outlet and from an outside spigot. Retest the water for bacteria one to two weeks later, and drink from another source until that test comes back clean.

Can I use pool shock to disinfect my well?

Pool shock is calcium hypochlorite, the same chemical in most well sanitizer packs. It works the same way as bleach: per EPA's disinfectant guidance, chlorine is less effective as pH rises, and it reacts with iron and organic matter before it reaches bacteria. If you use it, use a product labeled for potable water, never a pool blend with algaecides or clarifiers.

Why did the smell or slime come back a month after treating?

Because chlorine mostly burns the surface of the biofilm where the bacteria live, and the colony underneath regrows. This is the main reason our kit uses chlorine dioxide instead: it penetrates and strips the biofilm itself, per the manufacturer's published data.

How often should I treat my well?

Treat it after any positive bacteria test, after work on the pump or casing, after a flood, or when slime and odor show up. Test the water at least once a year, and let the test results, not the calendar, tell you when to treat.

How do you disinfect a well?

Disinfecting a well is the same job as treating it: fix any opening at the wellhead, put enough disinfectant into the well to reach the whole water column, run it through every faucet, let it stand, flush it out, and retest. The CDC says to leave chlorine in the well and plumbing for at least 12 hours and to wait at least 7 to 10 days before testing.

How do you sanitize a well?

Sanitizing a well is another name for disinfecting or treating it. The steps do not change: size the dose to the gallons in the well, circulate it through the plumbing, hold it for the contact time, flush, and retest for bacteria one to two weeks later.

How do you chlorinate a well?

Chlorinating a well means treating it with a chlorine product, usually unscented household bleach or calcium hypochlorite. Penn State Extension describes it as a fix for one-time contamination, and Ohio State Extension says to let the chlorinated water stand in the pipes 12 to 24 hours and retest about two weeks later. If bacteria keep coming back, a continuous disinfection system is the next step.

Sources

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Directions with our kit

Water per pouch: 10 liters for a 5-gram pouch, 24 liters for a 12-gram pouch. Your plan lists the amount to pour.

More than one pouch? Activate them one after another, steps 3 and 4 for each.

Follow all directions on the product label.

The first bacteria test bottle filling under the kitchen tap, its cap set aside

Step 1 of 11

What does a well even look like?

A typical well head is a capped pipe about six inches across that stands a foot or two above the lawn. Plenty of wells hide, so check these four spots.

A capped pipe in the yard

This is the most common look: a steel or plastic pipe about six inches across, knee-high, with a bolted cap on top.

In a covered pit

Older homes often keep the well below ground in a pit near the house, under a concrete lid you can lift.

Up through the basement floor

Some wells come up through the basement floor. Look for a capped pipe near your pressure tank.

Hidden on purpose

Some hide under a fake rock, a planter, or a wishing well. A lone ornament in the yard often marks the spot.

While you are out there, check the cap.

An old, cracked, or loose-fitting cap is how insects, mice, and surface water get into a well, and any of them can undo a fresh cleaning. The cap you want is called vermin proof: it clamps down on a rubber gasket seal and breathes through a screened stainless steel vent, so the well gets air as the water level moves and nothing else gets in. If yours wiggles, shows cracks, or has no screen under it, replace it. It is an inexpensive part protecting everything below it.