A national requirement for all water bodies to be swimmable all of the time is "impractical", Environment Minister Dr Nick Smith says.
But environmental groups have accused the Government of dodging tougher limits to address the country's freshwater woes.
In a lecture on freshwater management at Lincoln University last night, Smith said the Government was committed to improving the quality and swimmability of New Zealand's lakes and rivers, but was "cautious of regulatory requirements that are unworkable".
Most of the country's rivers breached the 540 E. coli count required for swimming during heavy rainfall, he said, and there were water bodies home to many birds whose E. coli made it impossible to meet the swimming standard without a massive bird cull.
"There are also rivers associated with geothermal activity that makes water quality unsuitable for swimming," he told the gathering.
"We also need to be open about the cost of our regulatory requirements on communities and the fact that many water bodies have long hydrological cycles that mean it is a long time before we see improvement."
Standards under the Government's National Policy Statement on Freshwater Management, set in 2014, includes a requirement for regional councils to manage freshwater bodies so people's health is safeguarded, and carries a bottom line that applies to "wading" and boating.
Smith said the Government was open to strengthening the national requirements on swimmability and had the Land and Water Forum working on options, he said.
"A lot of work is going into understanding the proportion of time our waterbodies meet the E. coli standards for swimming and how we can ensure it is improved."
Previous reports have shown around two-thirds of monitored freshwater sites in the country remain unsafe for recreational contact.
However, Smith said New Zealand's freshwater was "generally good" by international standards and added it was difficult from hard data to draw simple overall conclusions on freshwater quality.
Trends varied significantly from river to river, it took years of data to make meaningful comparisons and quality was measured by different indicators.
"The best summary I would give of the data on overall fresh water quality throughout New Zealand is that bacterial contamination and macroinvertebrates are unchanged during the past 25 years, dissolved phosphorus is improving and nitrate levels are generally deteriorating," he said.
The worst water quality was in urban areas but these are comparatively small in total area, while the most significant declines were in more intensively farmed areas and were caused by minimum flows being too low and levels of nutrients or sediment being too high, he said.
"The good news on water quality is that our systems for dealing with point sources of pollution under the Resource Management Act (RMA) are generally working well.
"There has been a huge reduction in pollution entering our lakes and rivers from dairy sheds, factories and town effluent systems, and billions has been spent on upgrades."
The Government had several clear policy views on how to improve freshwater management, he said, including a stronger national direction and more collaboration between parties.
"I do not buy the rhetoric that farmers are environmental vandals and environmentalists and recreationists are economic imbeciles."
By 2030, he wanted the Government's freshwater reforms to have resulted in consistent data showing rivers, lakes and aquifers were cleaner and healthier, an agricultural sector using water and nutrients more efficiently and the community understanding the value of rivers and lakes.
Smith also commented on the gastro outbreak in Havelock North that left thousands of residents sick, calling it "a serious failure on which there are many tough questions that will need to be answered".
"The GNS data showing the infected water was less than a year old in an aquifer source where it should be more than 50 suggests a localised surface water breach of the well's integrity, but we should be cautious of drawing conclusions ahead of the independent inquiry."
Swimmable bottom line "about looking after people" - campaign group
The Green Party today hit out at Smith for citing pollution from birds and geothermal activity as reasons for not committing to swimmable rivers.
"We asked the regional councils how many waterways in their area are affected by birds and geothermal or volcanic activity, and the numbers are minimal," the party's water spokesperson, Catherine Delahunty, said.
"Dr Smith is just using this as an excuse for why he won't commit to swimmable rivers.
"Protecting our rivers so they are safe for swimming doesn't fit the Government's view that water is a resource to be exploited for economic gain above all else."
She said the party had solutions to tackle pollution and was touring the country talking to communities about them.
"The response has been overwhelmingly positive - people really want our rivers to be safe for swimming and are prepared to do the work to get them there.
"It's a shame the Government doesn't have the same commitment or passion for our environment."
Freshwater campaign group Choose Clean Water, which this year presented Parliament with a 12,000-strong petition demanding action, has also called for all of New Zealand's waterways to be safe to swim in.
The group said New Zealanders had "resoundingly" called for "swimmable" to be the bottom line and that the Government should respond by putting in place legislation that protected clean safe freshwater and people's health.
In the recent freshwater public consultation, three quarters of New Zealanders who made submissions raised swimmability as a key concern, while 72 per cent also called for "swimmable" to be the national bottom line.
"It's good to hear the minister acknowledge the huge public support for a swimmable bottom line," spokesperson Marnie Prickett said.
"A swimmable bottom line is about looking after people and taking responsibility for our part in freshwater pollution, not looking to the birds as an excuse to keep polluting and making things worse."
NZ cycle tour highlights global water crisis
Meanwhile, French campaigner Theo Rohfritsch has arrived in New Zealand as part of a 14-month, 25,000km world tour to highlight the global water crisis.
Tomorrow, the 24-year-old sets off from Auckland for Invercargill on his bamboo bike, finishing his final 1600km leg of KPMG-backed initiative Cycle for Water.
One third of the world's population did not have access to adequate water sanitation, and more than 650 million people do not have access to safe drinking water.
The water crisis was the No 1 global risk based on impact to society, according to the World Economic Forum.
"Water is something many of us take for granted, yet clean, safe drinking water is key to healthy lifestyles," Rohfritsch said.
"I can't wait to share this message with a generation of young Kiwis on my journey through your beautiful country in my quest for change to be made to help combat the global water crisis."
KPMG has also just published a report looking at the importance of water to New Zealand.
The accountancy firm's executive chairman, Ross Buckley, said the report examined the impact our growing population would have on our natural water resources, and made a call to consolidate water management.
"We are fortunate to have a plentiful supply of water, and while we are not immune from water challenges, it is beholden to us to respect and value our 'liquid gold'.
People can follow Rohfritsch's journey through New Zealand here.