The number of private wells contaminated with a harmful strain of E.coli which can lead to kidney failure has doubled in the last year.
A drinking water report has revealed that the quality of public water supplies improved last year, with high levels of human waste found in supplies down by almost 90% since 2005.
However, the Environmental Protection Agency (EPA) said private wells are a growing cause for concern, with instances of the Verotoxigenic Escherichia coli (VTEC) bug doubling.
Valerie Doyle, senior inspector in the Office of Environmental Enforcement, said recent bad weather and heavy rain can contaminate wells.
"Any form of E.coli is an indicator of fecal matter in the water supply, and VTEC is a harmful form of E.coli," she said.
"It may cause gastroenteritis, but its toxins can lead to far more serious consequences including kidney failure.
"We would urge the owners of private wells to test them carefully, given the bad weather we've had. Owners should ensure that they are designed, located, installed and maintained properly."
The EPA issued 26 boil water notices and five water restrictions (serving approximately 40,000 people) were put in place by 15 water service authorities, while 23 legally binding directions were issued to eight authorities.
It also said there are 183 water supplies in need of remedial works, down 339 in the four years, with 90 set to be complete by year-end.
The EPA said its report, which is based on results from 250,000 monitoring tests, shows public water supplies serving more than 80% of the population have improved year on year since it created a remedial action list more than four years ago.