Disinfecting a flooded well

21.1 Why treat every flooded well as contaminated?

Because you cannot see what got in. AgriLife's guide to flooded wells says to assume the water in a flooded well is contaminated, and not to use it for drinking, cooking, making ice, brushing teeth or bathing. Floodwater around Wharton carries field runoff, septic overflow and street water, and it can enter through a loose cap, a cracked seal or the casing itself.

The well does not need to be under a lake for this to apply. AgriLife's 2019 flood preparation guide says not to drink, brush teeth or cook with well water if the well was submerged even for a short time. Its older guide adds that a well inside a pit can flood even when the yard around it stays dry.

21.2 Who should do the shock chlorination?

A licensed driller, or a licensed pump installer. AgriLife says plainly that it is strongly recommended to hire a licensed water well driller to shock chlorinate a flooded well, because drillers have stronger products and the right equipment. The EPA says drilled, driven and bored wells are best disinfected by a well or pump contractor, and CDC says wells should be disinfected by a contractor because of safety concerns.

Those safety concerns are real. Opening the well means working at the casing, often next to the pump's wiring and a pressure switch that may still be damp. CDC's May 2025 page on disinfecting wells warns not to enter a well pit because gases can build up there. TDLR licenses drillers and pump installers, and Well pumps and pressure tanks after a flood covers checking a license.

21.3 What does the job involve?

It follows a published procedure. AgriLife's shock chlorination guide, ESC-059 from August 2019, and CDC's page both lay out the steps, and they look roughly like this in outline:

1. The well is pumped until the water runs clear, once the pump and wiring have been cleared to run.
2. Softeners and filters are put on bypass so the chlorine does not damage them.
3. The contractor opens the well and adds a chlorine solution sized to the well's diameter and water depth.
4. The chlorinated water is circulated in the well and then drawn to every faucet in the house until it smells of chlorine.
5. The water sits in the well and pipes for the contact time the chosen procedure sets.
6. The system is flushed, outdoors first, with the water sent away from the septic system, gardens and any creek or ditch.

This book does not print bleach amounts or contact times. AgriLife's and CDC's tables give quite different amounts for the same well, and their contact times differ too, so a contractor picks one procedure and follows it all the way through. AgriLife also notes that its do-it-yourself method is for wells with a working submersible pump only; a jet pump or a damaged system needs a contractor regardless.

21.4 What is your part on the day?

Mostly keeping safe water on hand and running taps when asked. Table 21.1 splits the work.

Task	Who does it
Check pump wiring and controls before power goes back on	Licensed electrician or pump contractor
Open the well, add chlorine, close and seal it	Licensed water well driller or pump installer
Put the softener and filters on bypass	Contractor, or you if asked and the unit and floor are dry
Open each faucet when the contractor asks, then close it	You
Keep children and pets away from the wellhead and flush water	You
Collect a bacteria sample in a lab's sterile bottle	You, or the contractor
Supply drinking water until the lab result is clear	You

Keep a supply of sealed bottled water in the house through the whole process and the wait after it. AgriLife lists bottled water, water boiled for one minute, or water from a source known to be safe. If a public notice in your area gives a longer boil time, follow the notice.

21.5 What can chlorine not fix?

Chemicals and broken parts. AgriLife's flooded-well guide says disinfection does not remove fuels, oils, pesticides, heavy metals or other non-biological contamination. CDC adds that water with fuel or chemicals in it will not be made safe by boiling or disinfection. If you smell fuel at the tap or saw an oil sheen on the floodwater around the well, tell the contractor and the lab.

A damaged well will not hold the treatment either. If pressure falls off after the pump restarts, AgriLife reads that as possible damage and sends owners to a certified contractor; shock chlorination will not work until that is fixed. Wells where disinfection keeps failing may need cleaning before they are treated again, as the Texas Well Owner Network's tri-fold guide notes.

21.6 When can you drink the well water again?

Only after a lab test shows no total coliform and no E. coli. The Texas Well Owner Network puts it in capitals: do not drink the water until it has been tested for both. CDC says to wait at least 7 to 10 days after disinfection before sampling, so the chlorine is fully flushed and does not hide bacteria.

That test, and the repeat tests after it, are the subject of Testing well water after a flood. If the septic system also flooded, it can keep feeding bacteria toward the well, so read A flooded septic system as well. To make the next flood less likely to reach the water, see the wellhead chapter on sanitary caps and raising the casing.

Questions readers ask

Can the household bleach in the laundry room be used for this?

AgriLife's procedure calls for unscented household liquid bleach less than 6 months old, and CDC notes that bleach strength is generally between 5 and 9 percent. Scented, splash-less or old bleach is not what the procedures assume, so ask the contractor what they will use.

Where should the chlorinated flush water go?

Away from the septic system, plants and any body of water, AgriLife says. CDC suggests draining it onto an area without plants, such as a driveway. Keep it out of ditches that feed creeks like Peach Creek or Caney Creek.

Is the water heater part of the job?

Yes. AgriLife's older flood guide says to flush the household plumbing, including the water heater, as part of cleaning a flooded well. If the heater itself was under water, it is not reused; see the chapter on flooded water heaters.

Will one disinfection be enough?

Often, but not always. CDC says that if any coliform shows up in the follow-up test, repeat the disinfection and test again. If bacteria keep returning, call the local health department.

Does flood insurance pay for disinfecting the well?

FEMA's Dwelling Form lists wells among underground structures that are not insured, as the form stood on FEMA's site on 11 Nov 2026. Check with your agent and see Flood insurance and plumbing damage.

What this chapter rests on

The procedure described here follows AgriLife's ESC-058, ESC-059 and ER-011 guides, the Texas Well Owner Network's tri-fold, CDC's well disinfection page and the EPA's flood guidance for well owners, checked on 11 Nov 2026. Bleach tables and contact times are left out on purpose, because the sources disagree and the work belongs to a licensed contractor. We found no Texas DSHS well disinfection page to compare.

Notes to chapter 21

1. Texas A&M AgriLife Extension — ER-011, Decontaminating Flooded Wells (2006) · assume contamination, wells in pits, chemicals not removed, flush water heater · checked 11 Nov 2026
2. Texas A&M AgriLife Extension — ESC-058, How to Ready Your Well for the Next Flood (2019) · submerged even briefly, hire a licensed driller to shock chlorinate · checked 11 Nov 2026
3. Texas A&M AgriLife Extension — ESC-059, How to Disinfect a Water Well Through Shock Chlorination (2019) · outline of steps, submersible pumps only, pressure drop, flush water placement, safe drinking water options · checked 11 Nov 2026
4. Texas Well Owner Network — How to Disinfect a Private Well System in 7 Steps (2017) · no drinking until coliform and E. coli test, cleaning if disinfection fails · checked 11 Nov 2026
5. CDC — How to Disinfect Wells After an Emergency · contractor recommended, well pit gases, bleach strength, 7 to 10 day wait, repeat if coliform found · checked 11 Nov 2026
6. US EPA — What to Do After the Flood (816-F-05-021) · wells best disinfected by a well or pump contractor · checked 11 Nov 2026
7. TDLR — Water Well Drillers and Pump Installers · licensing of drillers and pump installers · checked 11 Nov 2026
8. FEMA — NFIP Dwelling Form F-122 (2021) · wells listed as not insured · checked 11 Nov 2026