A top Canterbury health official says the regional council needs to act to turn around what he calls the juggernaut problem of nitrates contaminating the water supply.
A report into the quality of groundwater in Canterbury shows some sources have unacceptable levels of nitrate.
The report says Canterbury groundwater is widely used as a source of untreated drinking water. It found nitrate levels have been increasing in about a third of the wells tested in the past decade.
The regional council tested 289 wells for various chemicals in its annual groundwater survey, carried out from September to December last year.
Of the wells tested, 33 were found to have nitrate levels that exceeded the maximum acceptable level for drinking water standards, and increase on the previous survey. Most of those wells are privately owned.
The council's report also shows E.coli was detected in 36 wells.
Canterbury medical officer of health Alistair Humphrey says the nitrate is a risk to infants, causing blue baby syndrome, and an important indicator of other water quality problems.
"Nitrates are the canary in the mine for worse problems with your water. Essentially, it means your water is polluted and other micro-organisms for example can contaminate your water following on from nitrate.
Dr Humphrey says the increase can be blamed on more intensive farming and irrigation.
"What we're seeing now is the effect of intensification, which not only affects our health, but of course it's a threat to our balance of payments if we end up having to treat all our water, which will cost us millions of dollars a year."
The Canterbury District Health Board is working with the regional council on the region's water management strategy, he says.