The Government has set a target of making 90 per cent of New Zealand's rivers and streams safe for swimming by 2040.
That means all waterways will have to meet the safe standard for E.coli contamination 80 per cent of the time.
Announcing the target in Auckland today, Environment Minister Nick Smith said 72 per cent of New Zealand's were currently "swimmable", according to a standard used in Europe and the US.
Raising that level to 90 per cent would require cleaning up 10,000km of waterways, and would cost Government, farmers and councils an estimated $2 billion. Farmers would have to build 56,000km of fencing.
Responding to the announcement today, the Green Party said the Government had "shifted the goalposts" for determining whether a river was swimmable.
Water spokeswoman Catherine Delahunty said a river used to be graded as "excellent" water quality if it had up to 260 parts of E.Coli per 100ml. The standard was now 540 parts of E.Coli per 100ml, she said.
Smith rejected this, saying the old threshold simply determined when increased monitoring was required, not whether a river was swimmable.
The Greens' water spokeswoman Catherine Delahunty said that meant there was 1 in 20 chance of getting sick in a river which had been approved as suitable for swimming.
The new target would be backed by national rules which require stock to be kept out of waterways and will make regional councils tighten their rules on sewage discharges.
Smith described the target as "ambitious" and said it recognised that New Zealanders expected to be able to "take a dip in their local river or lake without getting a nasty bug".
At present, the minimum standard for water quality in New Zealand is "wadeable". The standard will now be changed to "swimmable".
"It will return our rivers and lakes to a standard not seen in 50 years while recognising that our frequent major rainfalls mean a 100 per cent standard is not realistic," Smith said.
The latest reports on water quality in New Zealand said around 60 per cent of rivers, streams and lakes were not safe for swimming.
But Smith said this was misleading because councils focused their monitoring on higher-risk sites.
The Government has used new data and monitoring to determine that 72 per cent of waterways were suitable for swimming.