Scientists are warning that our aquifers, the reserves of water under New Zealand's land surface, are being poisoned by intensive farming.

Although some aquifers are already contaminated, they say the worst is yet to hit because pollutants like nitrate, can take decades to get down to the drinking supply.

Canterbury University's Dr Jenny Webster-Brown says nitrate will loom large in New Zealand's future, but it's already a public health concern.

"I think we're definitely going to see things get worse before they get better."

Pregnant women and mums with young babies on private bores around Ashburton are advised to use bottled water as high nitrate levels can block oxygen in babies and cause the potentially fatal blue baby syndome.

Environment Canerbury test results show nitrate hotspots around Canterbury is growing.

Nitrate levels also exceed drinking standards in some areas of Southland, Waikato and Bombay due to market gardening leading to nitrate leaching.

But much of the nitrate in underground water now is from farming 30 or 40 years ago, which pre-dates dairy conversions.

Dr Webster-Brown says with the dairy industry now using nitrogen, levels will rise distinctly.

"We know that dairy as an industry tends to leach more nitrogen into the groundwater systems," she said.

"So we fully expect to see the nitrate in the groundwaters increasing markedly."

Nitrate can't be filtered or boiled out which means as the projected levels rise and travel deeper into our artesian aquifers, it will become more likely to pose problems to town supplies and for the booming water bottling industry.

At the moment though, all public water supplies in New Zealand are safe and comply with nitrate drinking standards.

However the Ministry reports that five smaller supplies are being closely monitored for nitrate.