Last checked: October 21, 2026

Well flooded? Inspecting, disinfecting, and retesting

Flood water can carry sewage, chemicals and sediment into a private well, and it can damage the pump and wiring. EPA, CDC and state health departments all give the same basic order: stay safe around the electrical system, get the well inspected, disinfect it, then test for bacteria before you rely on it again.

Did flood water reach your well?

The Minnesota Department of Health (MDH) splits it into two cases:³

• Flood water reached the well or covered the top of the casing. Assume the well is contaminated. Don't use the water for drinking, cooking or brushing your teeth until the flood water recedes and the well has been inspected (if needed), disinfected and tested.
• Flood water came within 50 feet of the well but didn't reach it. You may still want to test as a precaution. MDH says you don't need to disinfect before testing in this case.

EPA adds that wells more than 10 years old or less than 50 feet deep are likely to be contaminated, even if there's no visible damage.¹

Safety and inspection first

• Electrical system. After the water recedes and the pump and wiring have dried, EPA says not to turn the equipment on until a qualified electrician, well contractor or pump contractor has checked the wiring.¹ CDC says to turn off all electricity to the well area before clearing debris.²
• Debris and sediment. Fast flood water can loosen well hardware, damage the casing, and wear out pump parts with sediment. Some wells collapse.¹ If flood water may have entered the well directly, MDH says to have a licensed well contractor inspect it and clean out sediment. Using your own pump to do this could ruin it.³
• Well pits. CDC says not to enter a well pit, because gases and vapors can build up there.²
• Who should do the work. EPA says drilled, driven or bored wells are best disinfected by a well or pump contractor, because it's hard for an owner to do thoroughly.¹ CDC says working on a well after a natural disaster can be hazardous and should be done by a well or pump contractor.²

Disinfecting the well

Disinfection after a flood is a shock chlorination. Our shock chlorination guide covers the general points. Flood-specific points from the agencies:

• Bypass treatment equipment. EPA says to switch a water treatment system to bypass. CDC says to close the valves to a water softener, because the large amount of chlorine can damage it.¹²
• Contact time. EPA's flood sheet says to wait 6 to 24 hours.¹ CDC's emergency procedure says at least 12 hours.² Don't drink, cook, bathe or wash with the water during that time.¹
• Drain it safely. Run the chlorinated water out somewhere it won't harm plants, streams, lakes or septic tanks.¹²
• Follow one full procedure. Use your state or county's written instructions, CDC's How to Disinfect Wells After an Emergency, or EPA's What to Do After the Flood sheet, rather than mixing steps from different sources.

Chemicals are a different problem. CDC says water contaminated with fuel or toxic chemicals won't be made safe by boiling or disinfection. If the water smells like fuel or chemicals, contact your local health department and use bottled water.² EPA says disinfection doesn't protect against pesticides, heavy metals or other non-biological contamination.¹

Retesting after disinfection

• When to sample: EPA and CDC both say 7 to 10 days after disinfection, once all the chlorine is flushed out.¹²
• What to test: CDC says total coliform plus either E. coli or fecal coliform.² MDH says to ask an MDH-certified lab for a coliform bacteria test.³
• Until you have results: CDC says to boil the water (a rolling boil for 1 minute) or use another source.²
• Follow-up tests: CDC recommends another test in the next 2 to 4 weeks and another in 3 to 4 months, then bacterial testing at least twice a year, or more often if you suspect changes.²
• If bacteria show up: CDC says to disinfect again and retest, and to contact your local health department if bacteria keep showing up.² MDH says it may take several rounds.³

EPA warns that after a large flood, a well can become contaminated again for many months, including from failing septic systems, so repeated testing is needed.¹ Septic systems shouldn't be used right after a flood, because drain fields don't work until groundwater recedes.¹

For a lab, contact your local health department or your state's certified lab list (see your county page). CDC also lists EPA's Safe Drinking Water Hotline, 800-426-4791, for sampling information.²

Before the next flood

If a flood is coming, MDH suggests storing clean water, disconnecting the well's power, and having a licensed contractor install a watertight cap. If there's no time, cover the top of the casing with heavy plastic secured with electrical tape, strapping or wire (not duct tape). That keeps debris out, but you'll still need to disinfect and test. For wells that flood repeatedly, MDH suggests talking with a contractor about extending the casing above flood level.³

Where to get tested and treatment options

Related guides

• Shock chlorinating a well
• How often to test a private well
• How to read your well water test results
• How a private well works: drilled, dug and driven wells, pumps and pressure tanks