Bacteria in Well Water: Types, Testing & Treatment Guide

Bacterial contamination is the most common water quality problem affecting private wells. Unlike public water systems that continuously disinfect their water, your well draws water directly from an aquifer—and if bacteria find their way in, you could be drinking contaminated water without knowing it.

Understanding the types of bacteria that can contaminate well water, how to test for them, and what to do when you get a positive result is essential knowledge for every well owner. This guide covers everything from routine coliform testing to emergency disinfection procedures.

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If Your Water Tests Positive for E. coli

Stop drinking the water immediately. Do not use it for drinking, cooking, brushing teeth, or making ice. Use bottled water or boil water for at least one minute. E. coli indicates fecal contamination and the potential presence of dangerous pathogens.

Types of Bacteria in Well Water

Not all bacteria in water are dangerous, but testing helps identify potential contamination pathways and health risks.

Total Coliform Bacteria

Total coliform bacteria are a broad group that includes many species found naturally in soil, on plants, and in animal intestines. They're used as "indicator organisms" because their presence suggests that surface contamination may have reached your water.

What they indicate: Potential pathway for contamination from the surface
Health risk: Most coliforms themselves aren't harmful, but their presence is a warning sign
Standard: Zero total coliform per 100 mL is the goal for drinking water
Common sources: Soil, vegetation, surface water, damaged well components

A positive total coliform test doesn't mean you'll get sick, but it indicates your well needs attention. You should investigate contamination sources and disinfect the well.

Fecal Coliform and E. coli

E. coli (Escherichia coli) is a specific type of coliform bacteria found exclusively in the intestines of warm-blooded animals, including humans. Its presence definitively indicates fecal contamination.

What it indicates: Human or animal waste has contaminated your water
Health risk: High—indicates other pathogens are likely present
Standard: Absolute zero; any detection requires immediate action
Common sources: Septic system failure, animal waste, sewage contamination

E. coli Strains

Most E. coli strains are harmless, but some like E. coli O157:H7 can cause severe illness, bloody diarrhea, and potentially life-threatening kidney failure (HUS). Standard well water tests don't distinguish between strains—any E. coli detection should be treated as a health emergency.

Other Bacteria of Concern

While coliform testing is standard, other bacteria can also contaminate well water:

Bacteria	Source	Health Effects
Campylobacter	Animal feces, poultry	Diarrhea, fever, cramps
Salmonella	Animal/human waste	Gastroenteritis, fever
Legionella	Water systems, biofilms	Legionnaire's disease (pneumonia)
Pseudomonas	Soil, water	Skin infections, respiratory issues
Iron bacteria	Soil, naturally occurring	Not directly harmful; causes taste/odor issues

Iron Bacteria and Sulfur Bacteria

Iron bacteria and sulfur-reducing bacteria are common nuisance organisms in wells. While they don't typically cause illness, they create significant water quality problems:

Iron bacteria: Create rust-colored slime, stain fixtures, clog pipes, and cause metallic taste
Sulfur bacteria: Produce hydrogen sulfide gas, causing "rotten egg" odor
Treatment: Shock chlorination and ongoing disinfection may be needed

How Bacteria Enter Well Water

Understanding contamination pathways helps you prevent problems and identify sources when they occur:

Well Construction Defects

Damaged or missing well caps: Allow insects, animals, and debris to enter
Cracked well casing: Creates pathways for surface water and soil bacteria
Improper grouting: The seal between casing and surrounding soil fails
Casing corrosion: Metal casings can develop holes over time

Environmental Contamination

Flooding: Floodwater submerging the wellhead introduces massive contamination
Surface runoff: Water flowing toward and around the well carries bacteria
Septic system failure: Effluent can travel through soil to groundwater
Animal waste: Livestock, wildlife, or pet waste near the well

Aquifer Contamination

In some cases, the aquifer itself becomes contaminated, making treatment more challenging. This is more common in:

Shallow aquifers with poor natural filtration
Karst (limestone) geology with underground channels
Areas with dense septic systems
Agricultural regions with concentrated animal operations

Testing for Bacteria

When to Test

Annual bacteria testing is recommended for all private wells. Test more frequently if:

Your well has flooded or been submerged
Heavy rainfall or runoff has occurred near the well
You've completed well repairs or pump replacement
Anyone in the household has unexplained gastrointestinal illness
You notice changes in water taste, odor, or appearance
Your well is shallow (less than 50 feet)
A neighbor's well has tested positive
You're buying or selling property

How to Collect a Bacteria Sample

Proper sample collection is critical—contamination during sampling leads to false positives:

Use a sterile sample container provided by the lab
Choose a tap close to the well—avoid hoses, outside faucets with aerators, or water that's passed through treatment
Remove the aerator if sampling from an indoor faucet
Let water run for 2-3 minutes to flush standing water from pipes
Don't touch the inside of the bottle or cap
Fill to the indicated line—not overfilled
Keep sample cool and deliver to lab within 24 hours (ideally 6 hours)

Pro Tip: If testing after shock chlorination, wait at least 7-14 days and confirm no chlorine smell remains before collecting your sample. Chlorine residue can kill bacteria in the sample bottle, giving a false negative.

Understanding Test Results

Bacteria test results are typically reported as "present/absent" or as colony-forming units (CFU) per 100 mL:

Total coliform absent, E. coli absent: Your water meets safety standards
Total coliform present, E. coli absent: Retest recommended; investigate potential contamination sources
E. coli present: Stop drinking water immediately; disinfect well and retest

Treatment Options

Shock Chlorination

Shock chlorination is the standard response to bacterial contamination. It involves adding a high concentration of chlorine to the well to kill bacteria throughout the system.

Shock Chlorination Steps

1. Calculate chlorine amount: Based on well depth, diameter, and water depth
2. Prepare chlorine solution: Use unscented household bleach (sodium hypochlorite) or well-specific tablets
3. Pour into well: Remove well cap, add solution, wash down casing walls with hose
4. Circulate through system: Run each faucet until chlorine smell is detected, then turn off
5. Wait: Allow 12-24 hours contact time (don't use water)
6. Flush system: Run water outside (away from septic) until chlorine smell is gone
7. Retest: Wait 7-14 days, then test for bacteria

Continuous Disinfection Systems

If bacteria problems recur, ongoing disinfection may be necessary:

UV Disinfection

How it works: Ultraviolet light destroys bacteria DNA, preventing reproduction
Effectiveness: 99.99% reduction of bacteria, viruses, and protozoa
Cost: $500-1,500 for whole-house systems
Maintenance: Annual lamp replacement ($50-150)
Pros: No chemicals, no taste impact, effective against wide range of pathogens
Cons: Requires pre-filtration for turbid water; doesn't provide residual protection

Chlorine Injection

How it works: Continuously adds chlorine to water supply
Effectiveness: Excellent for bacteria; provides residual protection
Cost: $500-2,000 for residential systems
Maintenance: Regular chlorine solution refills, pump maintenance
Pros: Residual protection throughout plumbing; proven technology
Cons: May affect taste; requires ongoing chemical supply

Ozone Treatment

How it works: Ozone gas oxidizes and kills bacteria
Effectiveness: Very effective; stronger than chlorine
Cost: $1,000-3,000 for residential systems
Pros: No chemical residuals; effective against resistant organisms
Cons: Higher cost; no residual protection

Preventing Bacterial Contamination

Prevention is always better than treatment. These measures protect your well:

Inspect your well cap annually: Ensure it's secure, undamaged, and vermin-proof
Maintain proper grading: Land should slope away from the well
Keep contaminants away: No fuel storage, pesticides, or animal waste within 100 feet
Maintain your septic system: Pump regularly; repair problems promptly
Test water annually: Catch problems early
Inspect after storms: Check for damage or flooding

See our complete guide to preventing well contamination for more details.

Frequently Asked Questions

What does it mean if my well water tests positive for coliform bacteria?

Total coliform bacteria are a group of bacteria commonly found in soil, plants, and animal intestines. A positive coliform test doesn't necessarily mean your water will make you sick, but it indicates that your well may be vulnerable to contamination from the surface. It's a warning sign that disease-causing organisms could also enter your water. You should retest to confirm, then investigate potential contamination sources like damaged well caps, failing seals, or nearby septic systems. Shock chlorination is usually recommended.

Is E. coli in well water dangerous?

Yes, E. coli (Escherichia coli) in well water is a serious health concern that requires immediate action. E. coli specifically indicates fecal contamination—meaning human or animal waste has entered your water supply. While not all E. coli strains cause illness, their presence indicates other dangerous pathogens may be present, including disease-causing bacteria, viruses, and parasites. Do not drink the water until it has been disinfected and retests negative. Boil water for drinking and cooking, or use bottled water until the problem is resolved.

How often should I test my well water for bacteria?

Test your well water for bacteria at least annually, and more frequently in certain situations. Test immediately after flooding or heavy rain, after any well repairs or pump work, if you notice changes in water taste, odor, or appearance, if anyone in the household experiences gastrointestinal illness, after nearby septic system problems, and if your well is shallow (less than 50 feet). New wells should be tested before first use and again after 2-3 months of operation. Testing costs $20-50 through certified labs.

How do I disinfect my well after bacteria contamination?

Shock chlorination is the standard method for disinfecting a contaminated well. The process involves calculating the correct amount of chlorine based on well depth and diameter, adding unscented household bleach or well-chlorination tablets, circulating the chlorinated water through all fixtures, allowing 12-24 hours of contact time, flushing the system until chlorine is undetectable, and retesting 1-2 weeks later. For persistent contamination, you may need to identify and fix the contamination source first. Professional disinfection services are recommended for deep wells or recurring contamination.

What causes bacteria to get into well water?

Bacteria can enter well water through several pathways: damaged or missing well caps, deteriorated well casings with cracks or holes, improper sealing between casing and surrounding soil, flooding that submerges the wellhead, surface water runoff entering the well, nearby septic system failures, animal waste near the well, and contaminated aquifer conditions. Shallow wells (under 50 feet) are most vulnerable because surface bacteria can more easily reach the water. Proper well construction and maintenance are the best prevention.

Bacteria in Your Well Water?

Southern California Well Service can help with well inspection, shock chlorination, and ongoing disinfection solutions. We serve San Diego and Riverside Counties with expert well services.

Call (760) 463-0493 for Expert Help

Bacteria in Well Water