Scientists have found nitrates from North Canterbury agriculture may enter aquifers and as a result, Christchurch's drinking water could be affected.
However, the predictions are not likely to come into effect for between 50 to100 years and even then drinking water was expected to remain safe.
Council water supplies in Canterbury already contained nitrates at safe levels.
Dr Tim Davie, Environment Canterbury's chief scientist, says Christchurch's drinking water was "definitely" safe and would "continue to be so", but would not be as pristine.
Environment Canterbury (ECan) chairman Steve Lowndes said it was a "wake-up call" for local authorities responsible for the area's water.
"There will have to be a close appraisal of intensive farming north of the Waimakariri River in the light of the fact whatever emissions are incurred are possibly going to travel into the aquifers beneath northern Christchurch.
"They are going to have to look hard at the science."
ECan carried out a major investigation into the potential of nitrate contamination earlier this year, digging nine new wells, measuring groundwater quality and creating a model of what was expected in the future.
It discovered nitrates from land use north of the Waimakariri could enter deep groundwater systems and be transported underneath it to those systems to its south – undoing the assumption that the river acted as a natural barrier to potential contamination.
The study found no evidence of any current increase in nitrates in aquifers under the main part of Christchurch.
But it predicted nitrate levels in deep groundwater under the north of the city and the Belfast area would increase over 50 to 100 years – though water would still be safe to drink.
Nitrate levels under the main part of Christchurch could also increase, though there was greater uncertainty about this possibility, and again there would be no health concerns.
ECan chief scientist Dr Tim Davie said that while drinking water was "definitely" safe and would "continue to be so", it would not be as pristine – an issue he said was not being underestimated.
"The [expected nitrate] concentrations are still below the acceptable drinking water standard, but we recognise that people want to see the Christchurch drinking water and the Christchurch groundwater staying in a pristine state.
"That's why we're signalling that this work is there and we're starting to think about how we deal with it."
Nitrates were not dangerous to drink for most people and, unless found in high levels, did not present a health risk.
The primary risk was "blue-baby syndrome", which could be dangerous for infants. In parts of Mid Canterbury pregnant women were advised not to drink from private wells.
Davie said ECan's forecasts were based on a "worst-case scenario" that assumed intensive farming in North Canterbury remained the same as current practice.
"The modelling work is not saying that this will definitely happen, it is saying that it could happen if we are to continue with our land uses as they are.
"There's a pretty strong likelihood that things will change for the better, and that is likely to happen as part of the planning process.
"All of the planning work that has gone on in Canterbury over the last 10 years is about improving water quality."
Davie said the most effective way of combating nitrate contamination was through reducing its output from farming, with a "huge amount of science" work focused on that goal.
Chemically cleaning contaminated water would be "extremely expensive" and unnecessary, he said, given that drinking water would remain safe.
Groundwater took "decades" to move through the water system.
"If everything stopped now, if we concreted over the whole of the Waimakariri plains – which of course we're not going to – if we were to do something like that there would still be nitrate in the system that would come through for several years."
Canterbury District Health Board medical officer of health Dr Daniel Williams said while the study's findings were "reassuring for now", they were a reminder we needed to plan carefully for good water quality in the future.
A Christchurch City Council spokeswoman said the body would discuss the findings of the report "in due course".
This article has been sub-edited to remove assertions not supported by the evidence quoted.