The Parliamentary Commissioner for the Environment says New Zealand will have to make trade-offs when it comes to water quality.
In a report released on Tuesday, Jan Wright says even if technical fixes were to become available for dealing with every water quality problem, they would still cost a lot of money.
Dr Wright says her report aims to explain as simply as possible the cause and effect of water pollutants.
"It comes back to where can we get the most bang for our buck first and focusing on that. To understand how much bang you can get from a particular action, you do need to understand the science."
However, Dr Wright says science cannot tell policymakers how to make the compromises required to satisfy competing interests.
Federated Farmers president Bruce Wills says he is confident that with clever science and sensible forward planning, New Zealand can protect its environment and continue to pay the bills.
"By that I mean that we can actually continue to produce more from our land resources. But whilst doing that, I firmly believe we can do better around our environmental footprint and certainly have less impact on our water."
'True cost' not taken into account
But Green Party water quality spokesperson Eugenie Sage says such trade-offs do not take into account the true cost of environmental damage caused by industrial and agricultural activity.
"We have often seen in the farming community and agribusiness them saying we need more science before we act to control land uses or to clean up waterways.
"But as the Parliamentary Commissioner has noted, that call for more science can sometimes be used as a way of delaying difficult decisions."
Environment Minister Nick Smith says he is open to the idea of national water quality standards, but says implementation is likely to be complicated.
The Land and Water Forum which includes 58 key stakeholders will report to the Government in April on whether a national standard for water quality is the best way forward.
Dr Smith says water quality issues vary hugely around the country, there are no simple answers and any approach will need community action, education and good science.
Call for agribusiness to step up
Fish and Game says it is time for farmers and agribusiness to take responsibility for restoring water quality.
Chief executive Bryce Johnson, who also represents the Living Rivers Coalition, says there is already a huge amount of science on water quality, but a reluctance to implement it.
"We have got a significant problem with water quality in New Zealand. We need to do something about it and only now is industry starting to step up.
"Groups like Fonterra and New Zealand Beef and Lamb do have very special role here. They're in a classic position to be able to require a better performance in these areas."
Mr Johnson says he is heartened by the fact that the Environment Minister says he wants water policy to be science-led.
An advocacy manager for Forest and Bird, Kevin Hackwell, says water quality cannot be separated from the country's financial fortunes.
Mr Hackwell is also a member of the Land and Water Forum which is preparing the report for the Government.
He is confident that key stakeholders can come up with compromise solutions that will balance competing interests.