The Upstate does not flood the way the coast does, but when it does, it does it fast. Creeks rise overnight, low corners of a lot become ponds, and well houses built decades ago in the lowest part of the yard end up standing in water. Hurricane Helene in 2024 showed how much damage a single storm can do across our area.

Here is the order to work through when the water goes down.

Step one: decide whether the well actually flooded

Water over the top of the casing	The well is contaminated. Do not drink, cook or brush teeth with it until it is disinfected and a test comes back clear.
Water pooled around the casing	Likely contaminated, especially if the cap is loose or the seal around the casing is old. Treat it as flooded.
Well house or tank room flooded	An electrical problem first. The switch, control box and connections need inspecting before power goes back on.
Ground wet but wellhead clear	Probably fine. Watch for cloudy or discoloured water over the following days, which would suggest surface water is getting in.

Step two: the electrics

The pump motor at the bottom of the well is sealed and spends its whole life underwater. A flood does not hurt it. What a flood does damage is everything above ground:

• The pressure switch, which has open contacts and fails readily after a soaking.
• The control box on three-wire systems, containing capacitors and relays.
• Wire splices and junction boxes, where mud and moisture lead to corrosion and shorts.
• Jet pumps, which sit above ground and have an exposed motor.

Components that have been underwater should be dried and checked, and in most cases the switch is simply replaced — it is inexpensive and a corroded one causes problems for months. See pressure switch and control box repair.

Step three: disinfect the well

Once the electrics are safe, the well needs disinfecting. The standard method is shock chlorination: chlorine added directly to the well, circulated through every pipe in the house, left for several hours, then flushed out. It is covered step by step in how to shock chlorinate a well.

Run any flushed water to the ground away from the septic system, not down the drains. Large volumes of chlorinated water can upset a septic tank.

Step four: test before you drink

Disinfection is not proof. Wait for the chlorine to clear, then have the water tested for coliform bacteria and E. coli. If the first test fails, the well is disinfected again and retested. A well that keeps failing usually has a physical route for surface water, such as a cracked casing or a failed seal. More on testing in well water testing in South Carolina.

Until a clear result comes back, use bottled water or boil water for drinking, cooking and brushing teeth.

Step five: fix the reason it flooded

• Extend the casing so the top sits well above ground and above likely flood level.
• Fit a proper sanitary well cap that seals and is vented with a screen.
• Regrade around the wellhead so water runs away from it.
• Raise electrics in a low well house off the floor.

See well cap replacement and wellhead protection.

What to remember

1	Water over the casing means unsafe. Until disinfected and tested.
2	Electrics first. Wet switches and control boxes stay off until checked.
3	The pump itself usually survives. It was built to sit underwater.
4	Disinfecting is not proof. A clear bacteria test is.
5	Raise the wellhead. So the next storm does not repeat it.

Frequently asked questions

Is my well water safe after a flood?

Not if floodwater reached or covered the wellhead. Assume it is contaminated until the well has been disinfected and a bacteria test comes back clear. Use bottled or boiled water in the meantime.

Will a flood damage my well pump?

A submersible pump is designed to run underwater, so the flood rarely harms the motor itself. The pressure switch, control box, wiring connections and any above-ground jet pump are what usually need checking or replacing.

Should I turn off my well pump during a flood?

If water is reaching the well house, pressure switch or wiring, yes, switch it off at the breaker, provided you can reach it safely without standing in water.

How do I disinfect my well after flooding?

Shock chlorination: chlorine is added to the well, circulated through the plumbing, left for several hours, then flushed out away from the septic system. Test for bacteria once the chlorine has cleared.

How long after a flood can I drink my well water?

Only after disinfection and a clear coliform and E. coli test. That usually takes a few days to a couple of weeks from the flood, depending on lab turnaround.

Can I boil flooded well water to make it safe?

Boiling kills bacteria and is a reasonable short-term measure for drinking and cooking. It does not remove fuel, chemicals or other contaminants floodwater can carry, so it is not a substitute for disinfecting and testing the well.

See emergency well pump repair, or what to do before help arrives if the water is off.