Bacteria in Well Water: Signs, Causes & Treatment

Your family takes a drink of water, and you assume it's safe. But here's the unsettling truth: over 15% of private wells in the U.S. contain bacteria at levels that could make you sick—and most well owners have no idea. Unlike city water that's constantly monitored and treated, your well is entirely your responsibility. That glass of water could look perfectly clear while harboring invisible threats like E. coli or coliform bacteria. Don't panic—but do keep reading. Understanding bacterial contamination is the first step to ensuring every sip from your tap is truly safe.

Signs Your Well May Have Bacterial Contamination

Here's the troubling truth: most bacterial contamination has no visible signs. Dangerous bacteria like E. coli are odorless, tasteless, and invisible. That's why testing is critical. However, some indicators suggest you should test immediately:

Health Symptoms

• Gastrointestinal illness: Unexplained stomach cramps, diarrhea, nausea, or vomiting
• Multiple family members sick: When several people in your household have similar symptoms
• Recurring illness: Repeated gastrointestinal issues that clear up when drinking other water
• Flu-like symptoms: Fever and body aches that could indicate bacterial infection

Environmental Warning Signs

• Recent flooding: Any flood event near your well area
• Standing water around wellhead: Poor drainage creating contamination risk
• Damaged or missing well cap: Easy entry point for contaminants
• Nearby animal activity: Livestock or wildlife waste near well
• Recent well work: Any repairs, pump replacement, or disturbance

Water Changes (Less Reliable Indicators)

• Sudden odor changes: Though most bacteria are odorless, some contamination creates smell
• Slime in fixtures: Biofilm buildup in pipes or on fixtures
• Discoloration: While usually mineral-related, can sometimes indicate problems

Types of Bacteria Found in Wells

Total Coliform Bacteria

Total coliform is a group of bacteria found throughout the environment—in soil, on plants, and in the intestines of warm-blooded animals. Their presence in well water doesn't necessarily mean you'll get sick, but it indicates a pathway for contamination exists. Think of coliform as a warning sign that harmful bacteria could enter your well.

Common causes of total coliform presence:

• Cracked or deteriorating well casing
• Improperly sealed well cap
• Surface water entering the well
• Shallow well depth
• Recent construction or disturbance

E. coli (Fecal Coliform)

E. coli is a specific type of coliform that only comes from fecal matter—human or animal waste. Any presence of E. coli means your water has been contaminated with sewage or animal waste and should not be consumed until treated and confirmed clear through testing.

E. coli contamination sources:

• Failing septic systems
• Livestock operations nearby
• Wildlife accessing the well area
• Sewer line breaks or leaks
• Flooding carrying animal waste

Other Harmful Bacteria

Beyond coliform, wells can harbor other dangerous bacteria:

• Legionella: Causes Legionnaires' disease, especially dangerous in hot water systems
• Pseudomonas: Opportunistic pathogen causing various infections
• Iron bacteria: Not typically harmful but creates slimy deposits and bad taste
• Sulfur bacteria: Creates rotten egg smell and can affect water quality

What Causes Bacterial Contamination?

Well Construction Issues

• Cracked casing: Allows surface water and contaminants to enter
• Inadequate grout seal: Gap between casing and surrounding soil
• Damaged well cap: Missing, cracked, or improperly sealed caps
• Shallow depth: Wells less than 50 feet more vulnerable to surface contamination
• Old dug wells: Large diameter, shallow wells are highest risk

Environmental Factors

• Flooding: Surface water overwhelms well protection
• Heavy rainfall: Saturated soil pushes contaminants toward well
• Poor drainage: Standing water around wellhead
• Proximity to contamination sources: Septic systems, feedlots, fertilized fields

Human Activities

• Well work without disinfection: Introducing bacteria during repairs
• Improper maintenance: Neglecting regular inspections
• Septic system issues: Failed or poorly maintained systems
• Agricultural runoff: Manure application near wells

How to Test for Bacteria

Getting an Accurate Test

Proper sampling technique is critical for accurate results. We recommend professional sampling, but if collecting yourself:

1. Use a sterile container from a certified lab
2. Remove any aerators or filters from the tap
3. Sterilize the faucet opening with a flame or alcohol
4. Run water for 2-3 minutes before collecting
5. Fill container without touching inside surfaces
6. Keep sample cold and deliver to lab within 24 hours

Understanding Test Results

• Total Coliform: Absent (0) – Ideal result, water is safe
• Total Coliform: Present – Indicates contamination pathway; retest and investigate
• E. coli: Absent (0) – Required for safe drinking water
• E. coli: Present – Do not drink; immediate treatment required

Treatment Options for Bacterial Contamination

Shock Chlorination (One-Time Treatment)

Shock chlorination involves introducing a strong chlorine solution into your well to kill bacteria throughout the system. This is typically the first line of treatment for bacterial contamination.

Process:

• Calculate chlorine needed based on well depth and diameter
• Pour chlorine solution directly into well
• Circulate through all plumbing fixtures
• Let sit 12-24 hours
• Flush entire system until chlorine is gone
• Retest after 1-2 weeks

Cost: $150-$400 for professional service

Best for: One-time contamination events, post-repair disinfection

UV (Ultraviolet) Disinfection

UV systems use ultraviolet light to kill bacteria as water flows through. They provide continuous treatment without chemicals.

Advantages:

• No chemicals added to water
• No change to taste or odor
• Effective against bacteria, viruses, and parasites
• Low operating cost (lamp replacement annually)

Considerations:

• Requires clear water (sediment blocks UV light)
• No residual protection in plumbing
• Lamp must be replaced annually

Cost: $500-$1,500 installed

Continuous Chlorination

For persistent contamination problems, continuous chlorine injection provides ongoing treatment.

Systems include:

• Chemical feed pump
• Chlorine solution tank
• Contact tank for adequate treatment time
• Optional carbon filter to remove chlorine taste

Cost: $1,000-$3,000 installed

Best for: Ongoing contamination issues, high-risk well locations

Well Repair or Replacement

If contamination persists after treatment, the source must be addressed:

• Casing repair: Fix cracks or install liner
• Grout seal repair: Seal gaps around casing
• Well cap replacement: Install sanitary well seal
• Deepen well: Drill to safer aquifer depth
• New well: If existing well can't be adequately protected

Preventing Bacterial Contamination

Maintain Your Wellhead

• Inspect well cap annually for damage
• Keep wellhead at least 12 inches above ground
• Ensure proper grading slopes away from well
• Keep area clear of debris and vegetation
• Fence to keep livestock and pets away

Protect Your Aquifer

• Maintain septic systems properly (pump every 3-5 years)
• Keep minimum 100-foot distance between well and septic
• Avoid chemical use near well area
• Don't mix or dump chemicals near wellhead
• Properly dispose of household hazardous waste

Test Regularly

• Annual bacteria testing at minimum
• Test after any flooding
• Test after well or pump work
• Test if anyone has unexplained illness
• Test after extended non-use

When to Call a Professional

Contact a well professional immediately when:

• Your water tests positive for E. coli
• Coliform bacteria persists after shock chlorination
• You notice visible damage to your well
• Your well has flooded
• You need help identifying contamination sources
• You want to install ongoing treatment systems

Learn more about our water testing services and well maintenance programs.

Frequently Asked Questions