About 120 households in rural Otago are being warned not to drink the water from their bores after testing found high levels of the faecal bacteria E. coli.
Otago Regional Council chief executive Sarah Gardner said the worst result in the Lower Waitaki plains area was from March.
"The levels have spiked at quite a high number - I understand at around 150 [colony forming units - or viable cells - per millilitre] above what the drinking water standard is.
"At other times, they have been relatively close to the standard - but not as close as they should be."
The safe level for drinking water is "less than one" colony forming unit per millilitre.
"Bore owners had been sent emails warning them not to drink the untreated water and would receive follow up letters in the post," Mrs Gardner said.
The council was still investigating the source of the contamination.
The Southern District Health Board Medical Officer of Health, Keith Reid, said residents must not drink untreated water or use it for cooking.
"Exposure to E. coli can have serious and long-term effects and is especially dangerous for children, older persons and people with compromised health. Gastroenteritis symptoms usually develop within 12 to 18 hours and include severe abdominal cramping, vomiting, and diarrhoea," Dr Reid said.
"The only way to be certain of having safe drinking water is to have drinking water treated. That means disinfected using chlorination, ozonation, boiling or filtration."
However, he said there had not been any reported increase in gastro-bugs in the region over the last 12 months.
More than 5000 people were hospitalised with gastroenteritis in 2016 after drinking contaminated water in Havelock North.