E. coli in Well Water

E. coli (Escherichia coli) is a type of bacteria found in the intestines of humans and warm-blooded animals. Most strains are harmless and part of normal gut flora. Some strains can cause illness.

In water testing, E. coli serves as an indicator organism. Labs do not test for every possible pathogen in your water because that would be expensive and impractical. Instead, they test for E. coli because finding it strongly suggests fecal contamination has occurred.

An important point that surprises many homeowners: a routine E. coli test does not tell you whether a dangerous strain is present. It tells you that feces may have entered your water and that you should treat the water as unsafe until the problem is fixed. (CDC)

Total coliform bacteria are found throughout the environment. They can enter wells from soil, plants, or surface water. Most total coliform are harmless. A positive test means your well may be vulnerable to contamination, but it does not necessarily mean fecal matter is involved.

E. coli is different. It lives specifically in intestines. Finding E. coli in water means waste from a person, livestock, wildlife, or pet likely made its way into your well.

This distinction matters for how you respond:

• Total coliform positive, E. coli negative: Investigate and retest, but not necessarily an emergency.
• E. coli positive: Stop using the water for drinking and cooking immediately.

For public water systems, the EPA Maximum Contaminant Level Goal for E. coli is zero. A confirmed positive triggers urgent action. (EPA)

E. coli enters well water when there is a path for fecal contamination to reach your water supply. Common sources include:

Wellhead Problems

The most common entry point. Contamination can get in through:

• Damaged or missing well cap
• Unscreened vents that let insects or animals in
• Casing that sits too low, allowing surface water to pool around it
• Cracks or gaps in the casing or seal

Flooding and Heavy Rain

Flood water can carry waste directly to your wellhead. Even heavy rain without flooding can push contamination through weak seals. Public health agencies commonly recommend testing after any significant flood. (CDC)

Septic Systems

A failing or poorly located septic system can contribute bacteria to groundwater. Even functional systems may pose risk if they are too close to the well or if soil conditions allow contamination to travel.

Animal Waste

Nearby livestock, feedlots, or manure storage can increase contamination risk, especially during rain or when groundwater levels are high.

Recent Well Work

Opening a well for repairs or pump replacement can introduce bacteria if proper sanitation is not maintained. Wells should be disinfected after any service that opens the system.

Most bacteria tests include both total coliform and E. coli. The CDC recommends testing private well water for bacteria at least once a year. (CDC)

Test sooner if:

• Your area experiences flooding
• You notice changes in water clarity, taste, or odor
• Anyone in your household has unexplained gastrointestinal symptoms
• Your well has been opened for repairs
• You are buying a home with a private well
• A baby joins your household or someone becomes pregnant
• Your septic system backs up or shows signs of problems

If your well has a history of bacteria problems, consider testing more often, such as every six months or after any heavy rain event.

Bacteria tests require careful sample collection. Unlike chemical tests, bacteria samples are time-sensitive and easy to contaminate during collection.

Use a Certified Lab

The CDC recommends state-certified laboratories for well water testing. Your local health department can provide a list of approved labs. (CDC)

Follow Collection Instructions Exactly

• Use only the sterile bottle provided by the lab
• Do not rinse the bottle or touch the inside of the cap
• Remove the faucet aerator if instructed
• Run the water briefly before collecting
• Fill to the marked line without overflow

Get the Sample to the Lab Quickly

Bacteria samples typically need to reach the lab within 24 to 30 hours. Keep the sample cold during transport. Late or warm samples can produce unreliable results.

Cost and Turnaround

A basic bacteria test (total coliform plus E. coli) typically costs $20 to $50. Results usually come back within 2 to 5 days.

Most lab reports show bacteria results as "Present" or "Absent" (sometimes "Detected" or "Not Detected").

Understanding the Standard

For public water systems, the EPA Maximum Contaminant Level Goal for E. coli is zero. Private wells are not regulated by federal rules, but zero remains the target. Any detection of E. coli in drinking water requires action. (EPA)

What Your Results Mean

• E. coli absent, total coliform absent: Your water passed. Continue annual testing.
• E. coli absent, total coliform present: Your well may have a vulnerability. Retest and investigate.
• E. coli present: Fecal contamination is likely. Stop using the water for drinking and cooking immediately.

An E. coli positive result requires immediate action. Do not wait to see if symptoms appear.

Step 1: Switch to Safe Water Immediately

Use bottled water or another safe source for: (WI DHS)

• Drinking
• Cooking and food preparation
• Brushing teeth
• Washing produce
• Making ice
• Mixing baby formula

Step 2: If You Must Use Tap Water, Boil It

Boiling kills bacteria and viruses. The CDC recommends bringing water to a rolling boil for one minute (three minutes at elevations above 6,500 feet). (CDC)

Important limitation: Boiling does not remove chemical contaminants. If your water also has nitrate or arsenic, boiling will concentrate them. Use bottled water if you have not tested for chemicals recently.

Step 3: Contact Your Health Department

Your local health department can help interpret results and recommend next steps specific to your area. They may know about local contamination patterns or offer guidance on well disinfection. (CDC)

Step 4: Identify and Fix the Source

Walk through these questions:

• Was there recent flooding or heavy rain?
• Has the well been opened for repairs?
• Is the well cap damaged or loose?
• Are there cracks in the casing or seal?
• Is water pooling around the wellhead?
• Is the septic system functioning properly?

Fix obvious problems before moving to disinfection.

Step 5: Disinfect the Well

Shock chlorination is the standard approach for killing bacteria in a well. State health departments provide specific instructions. (MN DOH)

If you are not comfortable doing this yourself, hire a licensed well contractor. Improper disinfection can damage well components or create hazards.

Step 6: Retest to Confirm the Fix

After disinfection, wait the recommended time and test again. Do not resume normal water use until you have a confirmed negative result. (MN DOH)

The CDC recommends additional follow-up testing 2 to 4 weeks after the first negative, and again in 3 to 4 months, to ensure the problem does not return. (CDC)

Prevention means keeping waste and surface water out of your well.

Protect the Wellhead

• Keep the cap secure, intact, and properly screened
• Ensure the ground slopes away from the well
• Keep the area clear of debris, standing water, and animal waste
• Inspect the wellhead at least twice a year

Maintain Your Septic System

Pump and inspect your septic system on schedule. Address backups or drainage issues promptly. A failing septic is one of the most common sources of bacteria contamination in private wells.

Test After Weather Events

Make it a habit to test your well after any significant flooding. It is easier to catch a problem early than to deal with ongoing contamination.

Keep Records

Save all lab reports. Note dates of well work, flooding, or septic maintenance. This history helps if you need to troubleshoot recurring problems.

Use a state-certified laboratory for bacteria testing. Your local health department can recommend labs that serve your area and may offer guidance on interpreting results.

Find well water testing providers in your state using our directory.