Coliform bacteria in your Florida well: how to shock chlorinate it

Sources last checked: November 3, 2026

If a lab test found coliform bacteria in your well, or your well was flooded, the standard fix is shock chlorination: putting a strong dose of chlorine bleach into the well and every pipe, letting it sit, then flushing it out and retesting. This guide follows the Florida Department of Health (FL DOH) procedure and notes where county health departments do it differently.

What a positive test means

FL DOH explains that most coliform bacteria aren’t harmful themselves, but their presence shows that surface contamination has found its way into the well, so disease organisms may be there too.¹ If the test finds E. coli or fecal coliform, FL DOH says the risk is more serious and the water should not be used for drinking, cooking or bathing.¹

Until you’ve disinfected and retested, FL DOH’s flood guidance is to boil drinking and cooking water at a rolling boil for at least one minute, or use bottled water.²

When FL DOH says to disinfect a well

FL DOH recommends disinfecting:¹

• When a lab test shows coliform bacteria.
• When the well has been flooded or was near flood waters.
• After installing or repairing plumbing or fixtures such as water softeners, faucets and filters.
• After well or pump repairs.
• When the water tastes different than normal or has a musty odor.
• When restarting a well, pump or plumbing that was shut off for a while, or after the system was drained or opened.

When it won’t fix the problem

FL DOH is clear that disinfection won’t solve contamination from a nearby source such as an improperly located septic system or animal feedlot, a well or plumbing system that is improperly built, located or damaged, or chemical contaminants like arsenic, nitrates, fuel or pesticides.¹ If the bacteria keep coming back after shocking, that points to one of these problems, and a licensed well contractor needs to find it.

Can you do it yourself?

FL DOH’s do-it-yourself procedure is only for wells with a submersible pump and a sanitary well seal with a removable threaded plug. If your pump sits in a well pit, you have a flowing well, or the seal has no threaded plug, FL DOH says to have a licensed well contractor or licensed pump installer disinfect it.¹

Hernando County’s health department adds a check before you start: no standing water near the well, a casing raised to at least ground level and in good condition, an airtight seal on top, and vent and wire holes sealed.³

How much bleach to use

FL DOH’s statewide fact sheet gives these amounts of plain, unscented laundry bleach (6.0% sodium hypochlorite), mixed into one gallon of water in a clean bucket:¹

Use a fresh container, because bleach loses strength over time, and never use bleach with fragrance or other additives.¹

Some county health departments use much stronger doses. Alachua County’s instructions, written to reflect the Florida Administrative Code rule for fixing a bacteria-contaminated private well (Rule 64E-8.007, which calls for keeping 50 mg/L of free chlorine throughout the system for three hours), use 2 gallons of household bleach mixed with about the same amount of water for an average three-bedroom home.⁴ Hernando County also lists 2 gallons of 5.25% bleach (or 1 gallon of 10% pool chlorine) for a typical 4-inch well.³ If your county health department has its own instructions, follow those.

Step by step (FL DOH procedure)

1. Power off and bypass. Disconnect water softeners and household filters, turn off the power and water supply, and drain the water heater.¹ FL DOH’s flood brochure notes chlorine isn’t effective in water above 105°F, and says to remove membranes, cartridges and filters and replace them afterward.²
2. Mix the solution. Add the bleach amount from the table to one gallon of water and mix. Wear gloves and goggles.¹
3. Cut pump power at the breaker or fuse, and leave it off until the chlorine is in the well.¹
4. Pour it in. Use a funnel through the threaded opening, avoid splashing the wire connections, and don’t use a siphon. Let it sit in the well for 30 minutes.¹
5. Pull it through every pipe. Turn the power back on and run each fixture one at a time (cold and hot taps, toilets, showers and tubs, outside faucets) until you smell bleach, then close it. Leave the chlorinated water in the plumbing for at least eight hours or overnight.¹
6. Flush it out. Run a garden hose from an outside faucet onto the ground until the chlorine smell is gone, then run each indoor fixture until it no longer smells of chlorine.¹ Hernando County says to flush the outside faucets first so you don’t send a flood of chlorinated water into your septic system.³
7. Reconnect treatment equipment. Disinfect your softener or filters per the manufacturer’s instructions, reconnect them, and refill and restart the water heater.¹
8. Retest before drinking. Make sure the chlorine is gone, then have the water tested by a DOH-certified laboratory before drinking it, cooking with it or making ice.¹

If you don’t smell chlorine when you first run the taps, FL DOH’s flood brochure says to re-chlorinate.² Alachua County’s lab tells homeowners to use the system for 3 to 5 days before collecting the follow-up sample.⁴

Safety: FL DOH warns that chlorine can damage eyes and inflame skin. Warn everyone in the house not to drink, cook with, shower or bathe in the water while it’s chlorinated.¹

Getting the retest

Your county health department can arrange sampling or point you to a certified lab; see our well testing section. FL DOH recommends testing for coliform bacteria at least once a year and whenever the taste, odor or appearance changes.¹

Related guides

• Slime, swampy smells or orange growth may be iron bacteria, which FL DOH also treats with chlorination plus physical cleaning: iron vs. iron bacteria stains.
• A rotten-egg smell after shocking? See the rotten-egg smell diagnosis and the water heater anode rod fix.
• Bacteria that keep returning, or a well you can’t open safely, is a job for a pro: see our installers section.

Sources