A report on freshwater from the Prime Minister's chief scientist, Sir Peter Gluckman, says some waterways have gone beyond a tipping point.
The report says some of our waterways will take more than a century to recover and even then they will never get back to their original state.
Opposition parties say it confirms that the government now has to acknowledge there are problems with freshwater.
The Environment Minister, Nick Smith, describes the report as fair and robust.
He says the Government and urban and rural New Zealand need to work together to tackle the country's fresh water problems.
Dr Smith told Morning Report the Government was moving on the issue, banning further agricultural intensification in 16 regions and investing $450 million into fresh water clean ups.
He says he doesn't take any "negative spin" from the report, but it shows our river pollution isn't a problem that arose yesterday and will take some time to fix.
The Prime Ministers 's chief scientist, Peter Gluckman, wrote the report and says it points out the 'multiple dimensions' of the issue.
"It's not just about swimability, it's not just about cows.
"There's lots of dimensions that we need to think about and we need to think in a more integrated way... The reality is, you have four, five, six million people living in New Zealand and their uses of that water will compromise the ecosystem."
Sir Gluckman's report found that agriculture is the main offender and says it will take time to repair the damage.