E. coli in water means faecal matter from people or animals has reached it, so the water is not safe to drink untreated until the source is found, the system is disinfected and a retest comes back clear. Total coliforms without E. coli are a warning rather than proof of sewage: something is getting into the borehole, tank or pipes, and it needs checking before it becomes a bigger problem.
Total coliforms, faecal coliforms and E. coli: what is the difference?
Labs don't test for every germ that could make you ill. They test for indicator bacteria, which are easy to grow and show whether disease-causing organisms could be present.
- Total coliforms are a broad group of bacteria found in soil, on plants and in faeces. Most won't make you sick, but SANS 241 uses them to check whether treatment is working and the system is clean and intact.
- Faecal coliforms, also called thermotolerant coliforms, are the subgroup that mostly comes from the gut of warm-blooded animals. The WHO accepts them as a stand-in where a lab does not test for E. coli directly.
- E. coli is the clearest sign of faecal pollution, and South Africa's drinking water standard treats its presence as an immediate, unacceptable health risk. Finding any means sewage or animal waste has reached the water, and with it the germs behind stomach illness.
- Heterotrophic plate count (HPC) is a general bacteria count. A high one means bacteria are multiplying somewhere in the system.
Reports based on the 2015 edition of SANS 241 often show "E. coli or faecal coliforms" as one line.
What SANS 241 allows
SANS 241 is the South African National Standard for drinking water. These are the microbiological limits most lab reports quote:
| Indicator | SANS 241 limit | Risk category | What a fail means |
|---|---|---|---|
| E. coli (or faecal coliforms) | Not detected per 100 mL | Acute health | Faecal contamination: do not drink it untreated |
| Total coliforms | 10 or fewer per 100 mL | Operational | Something is getting in: find it, disinfect, retest |
| Heterotrophic plate count | 1 000 or fewer per mL | Operational | Bacteria are growing in the system, often in a tank or filter |
| Giardia and Cryptosporidium | Not detected per 10 L | Acute health | Parasites that chlorine struggles to kill; UV inactivates them |
Coliform and E. coli counts are given per 100 mL, as MPN (most probable number) or CFU (colony-forming units) depending on the lab's method. "Not detected" is the only acceptable E. coli result.
Total coliforms are an operational parameter, a measure of how well treatment and the supply system are working rather than a direct health limit. A private borehole has no treatment works behind it, so stricter thinking makes sense: Health Canada sets the acceptable level for private wells at no total coliforms in a 100 mL sample. On a borehole, treat any coliform count as a reason to look for the cause.
What to do as soon as you get a positive result
- If E. coli was found, stop drinking the water untreated. Use bottled or municipal water, or bring it to a rolling boil, which the WHO says kills bacteria, viruses and parasites. That applies to cooking, brushing teeth and baby formula too.
- With total coliforms only, the urgency is lower. Health Canada says households can keep using the water while they wait for a retest. Boiling drinking water in the meantime is still the cautious choice, especially with a baby in the house.
- Retest to confirm. It is easy to contaminate a sample bottle by accident. Use a sterile bottle from the lab, follow the sampling steps in our guide on whether borehole water is safe to drink, and keep the sample cool: bacteria samples often have a holding time of about six hours.
- Watch your household's health. If anyone has diarrhoea lasting more than two days, bloody stools or signs of dehydration, speak to a doctor.
Find the source before you treat
Disinfection kills the bacteria there now, but if their way in is still open they come back.
Boreholes and wellpoints
Start at the borehole head. A cracked or loose cap, a damaged casing or water pooling around it after rain all give surface water a path down the hole. Then look further out: septic tanks, French drains, pit latrines, sewer lines and kraals are the usual sources of E. coli. Flooding and recent work on the borehole, such as a new pump, are common triggers. Shallow wellpoints draw water from close to the surface, so they are more exposed than a deep, sealed borehole.
Rainwater and storage tanks
A rainwater tank collects whatever is on the roof, including bird and rodent droppings. A Stellenbosch University study of household tanks in Kleinmond found Legionella, Salmonella and other potentially harmful bacteria in untreated tank water. Stored municipal water can go wrong too, because long storage, warmth and lost chlorine let bacteria regrow. Check the lid, screens and overflow for gaps, and see the tank cleaning steps in our rainwater filtration guide. If you are adding backup storage, the water tank size calculator helps you size it so the water turns over instead of standing for weeks.
Municipal water and your own plumbing
Treated municipal water normally carries a small chlorine residual, and metros such as Cape Town test thousands of samples a year against SANS 241. If a municipal tap tests positive, check whether it is fed through a storage tank or a filter that is overdue for a change: carbon removes chlorine but not bacteria, and an idle or saturated cartridge can grow them. Resample from a tap fed straight from the mains, and if that fails too, report it to your municipality.
Shock chlorination: what it involves
Shock chlorination is the standard first fix for a borehole, wellpoint or plumbing system that tests positive. It fills the whole system with a chlorine solution 100 to 400 times stronger than municipal water, leaves it to stand, then flushes it out.
- Fix the cause first, such as a broken cap or a leaking septic tank, or the bacteria will return.
- Bypass carbon filters and reverse osmosis units, because strong chlorine damages them. Check the manufacturer's instructions for softeners and geysers.
- Add the chlorine and run every tap in the house until you can smell chlorine, then close it.
- Leave it to stand for 12 to 24 hours.
- Flush through a hose onto gravel or a bare patch of ground, away from the septic tank and plants, until the chlorine smell has gone.
- Retest once the chlorine has cleared. Guidance ranges from a few days after the smell has gone to about two weeks. A further test two to three months later confirms the fix has held.
Strong chlorine needs care: never mix it with ammonia or acids, which release toxic gas, and wear gloves and eye protection. HTH (calcium hypochlorite) granules also react dangerously with oils and organic matter, so many owners leave the job to a borehole contractor or water treatment installer. Our borehole water treatment guide covers chlorine dosing and HTH in more detail.
When you need permanent disinfection
Shock chlorination is a one-off clean, not a treatment system. If bacteria come back, or the source can't be fixed, as with a shallow wellpoint or a roof-fed tank, drinking water needs continuous disinfection.
UV disinfection
A UV water filter is the usual final stage for drinking water on a private supply. It inactivates bacteria, viruses and parasites, including Cryptosporidium, which chlorine handles poorly, and adds no taste. A disinfection-grade unit (NSF/ANSI 55 Class A) delivers a UV dose of at least 40 mJ/cm². UV only works on clear water, so it needs a sediment filter ahead of it and water within the manufacturer's limits, typically turbidity below 1 NTU, iron below 0.3 mg/L, manganese below 0.05 mg/L and hardness below about 120 mg/L.
UV leaves no residual, so the pipes after it should be disinfected at installation, and stored water downstream is not protected. The lamp is replaced yearly even though it still glows, and after a power cut it needs about five minutes before water is drawn. On a house that runs on borehole or tank water, the UV unit usually sits at the end of a whole-house filtration system so every tap is covered.
Chlorine dosing
A dosing pump adds a steady, small amount of chlorine, which leaves a residual that keeps protecting water in tanks and pipes. The WHO benchmark is at least 0.5 mg/L of free chlorine after 30 minutes' contact. The trade-offs are the taste, the chemical handling and a carbon filter to take it out of drinking water.
What does not disinfect
Sediment and carbon cartridges do not remove bacteria, and reverse osmosis is not meant for microbiologically unsafe water unless it is disinfected before or after the membrane. Our guide to reverse osmosis vs UV explains where each fits.
Inside the City of Cape Town, borehole, wellpoint and rainwater may not be used for drinking, cooking or body washing without the City's approval, so check with the City first; elsewhere, check your municipality's by-laws.
Keeping the water clear after a positive test
- Test for bacteria at least once a year, and again after flooding, repairs to the borehole or pump, a change in taste, colour or smell, or when someone in the home is pregnant or a baby arrives.
- Keep the borehole head sealed and the ground around it free of standing water, animals and manure, with septic tanks well maintained.
- Service the treatment on schedule: a new UV lamp yearly, a clean quartz sleeve and fresh cartridges before they clog or go stale.
Frequently asked questions
Is it safe to drink water with coliforms in it?
Not if the coliforms include E. coli, because SANS 241 allows none in a 100 mL sample. Up to 10 total coliforms per 100 mL meets the SANS 241 operational limit, but on a private borehole or tank any coliforms mean something is getting in. Retest, find the cause and boil drinking water until a result comes back clear.
Does boiling water kill E. coli?
Yes. The WHO says bringing water to a rolling boil is enough to kill bacteria, viruses and parasites, so it is the right stopgap while you investigate. It does nothing about the source or chemicals such as nitrate, and boiled water needs clean, covered containers.
Will a water filter remove E. coli?
A standard sediment or carbon cartridge will not. Bacteria need a disinfection step, usually UV after sediment filtration, or chlorine dosing. Ultrafiltration membranes remove most bacteria, but on a contaminated private supply a correctly sized Class A UV unit is the usual answer.
Is E. coli in water dangerous?
It can be. Not every type of E. coli makes people ill, but its presence means faecal germs could be in the water, and some types cause severe stomach cramps and bloody or watery diarrhoea, and occasionally a serious kidney complication called haemolytic uraemic syndrome (HUS). If anyone in the home becomes ill, especially with bloody diarrhoea, speak to a doctor.
If your borehole or wellpoint has tested positive, our borehole water filtration page explains how we test and build a system. To get advice on your own results, send us the report with your water source, property type and area through the quote page, and we'll help with the next steps.
