By 2020, it was predicted 400,000ha of land would have been converted into dairy farms in the preceding 12 years - and even under optimistic assumptions, the report said, leaching would continue to increase.
Dr Wright said diffuse nitrogen, which was elusive and hard to stop entering waterways, was an especially difficult problem.
"Rolls Royce" mitigation efforts such as riparian planting - used to create buffer zones between waterways and land - and moving cattle to herd homes or stand-off pads when soils became sodden could capture much of the nitrogen.
But that was difficult for traditional farms running four or five cows to each hectare, or recently-converted farms where maximised volumes of milk were sought to service large loans.
Massey University freshwater scientist Dr Mike Joy believed that for mitigation measures to "catch up", fast-moving expansion of the industry would have to stop. Even then, he said, a "lag time" of nutrients moving through the soil meant they would continue to enter waterways for some time.
Putting more cows on each hectare of farmland also had consequences for our greenhouse gas emissions. Nearly half of our total emissions come from methane and nitrous oxide, predominantly from agriculture - and much of that from dairy farms.
Dairy cows, ruminant animals, naturally produced methane, while nitrous oxide stemmed from dung, urine and nitrogenous fertilisers.
But Federated Farmers president Bruce Wills still believed the golden balance between a high-performing dairy industry and a clean environment could be struck.
"I'm very confident that with good science, good technology and good management, we can have both."
The industry had agreed to a range of commitments, requiring farmers to exclude all cattle from waterways, manage nutrient loss and use water more efficiently.
Beyond these "low hanging fruit", Mr Wills said, farmers in regions where soils are lighter and more sensitive may have to keep cattle away from pastures more often - or reduce stock numbers.
"Rather than running four cows a hectare, they may have to back off to three, or three and a half," he said. "It may mean their gross profit is not as much, but as costs won't be as high, at the end of the day their net position might be better."
Finding scientific solutions to dairying's big environmental impact was a high priority, especially given international markets were becoming more aware of sustainability.
Just as important, the issue was the "front and centre" topic of farmers across the country, Mr Wills said.
"The conversation has changed. It's an evolving game and farmers are moving at pace, as we need to."
Prime Minister John Key also said striking a balance was "certainly possible". He cited Fonterra's campaign to fence 22,000km of waterways, the Government's National Policy Statement for freshwater management, and the quarter of a billion dollars in the process of being spent to clean up waterways.
"Obviously we are trying to make sure we concentrate more on prevention, rather than having to fix up waterways that are polluted," he said. "But I'm very confident we can balance our environmental responsibilities with the economic opportunities New Zealand has."
Morrinsville dairy farmer Stephen Allen, chairman of the Tatua Co-operative Dairy Company, felt farmers had embraced the challenge to become greener.
"I think the attitude of farmers is really positive - they just need to know how they do this."
Mr Allen said a combination of mitigation efforts, using "precision farming" technology to improve the use of nutrients and reducing stock rates or using more herd homes where needed would help.
"Will it stop it completely? I don't know - but I think we'll go a long way to improving things.
