A warning has sounded for New Zealand's dwindling freshwater species in a new report published today.

The Society for Conservation Biology's new report, titled Diagnosis and Cure, examines the decline of species living in fresh waterways and suggests solutions, including a law overhaul and improvements to policy, monitoring and management.

The authors noted that three quarters of the country's native freshwater fish, mussel and crayfish species, were now listed as threatened with extinction, something they blame on excessive nutrient run-off from over-intensive agriculture, extraction of water, river engineering, and human and industrial waste discharged to waterways.

The researchers cited commercial exploitation and exportation of many threatened and endemic species too.

One of the authors, Dr Mike Joy of Massey University's Institute of Agriculture and Environment, said the problems would be exacerbated by Government plans to increase agricultural production.

"There are even plans to increase development of our rivers and wetlands, exacerbating these problems," he said.

"It [fresh water quality] is a taonga of paramount importance and valued for its contribution to biodiversity, recreation, the economy and the overall wellbeing of New Zealanders."

The Government has set out core priorities and objectives to improve freshwater management in the new National Policy Statement for Freshwater Management.

These mean rivers and lakes now have minimum or "bottom line" requirements that must be achieved so the water quality is suitable for ecosystem and human health, and include a range of other actions for regional councils.

However, the authors argued the National Policy Statement did not go far enough and laid out six priorities to tackle the issue:

* Change legislation to adequately protect native and endemic fish species and invertebrates, including those harvested commercially and recreationally.

* Protect habitat critical to the survival of New Zealand's freshwater species.

* Include river habitat to protect ecosystem health in the National Objectives Framework for the National Policy Statement on freshwater.

* Establish monitoring and recovery plans for New Zealand's threatened freshwater invertebrate fauna.

* Develop policy and best management practices for freshwater catchments, which includes wetlands, estuaries and groundwater ecosystems.

* Establish, improve and maintain appropriately wide riparian zones that connect across entire water catchments.

"We can implement some real changes which will not only improve the freshwater environments for the species living in them, but also for us by providing clean water and wonderful places for fishing," co-author Dr Emily Elston said.

"We have to do something about the increasingly poor state of our rivers, lakes and groundwater resources. Business as usual is no longer an option."

The report has been endorsed by a list of freshwater scientists, including Professor Jenny Webster-Brown, the director of Canterbury University's Waterways Centre for Freshwater Management and Dr Gerry Closs, of Otago University.

The New Zealand Herald has approached a number of other leading scientists for their response to the report, as well as the Department of Conservation.

Parliamentary Commissioner for the Environment, Dr Jan Wright, earlier this year criticised several parts of the new National Policy Statement.

She argued that regional councils should prioritise protection of vulnerable water bodies and catchments, which were being affected by weeds, slime and algae that stemmed from nitrogen and phosphorus used on land as nutrients.

Those water bodies that were vulnerable to particular pressure should be considered first, because the cost and difficulty of restoring them would be that much greater, she said in June.

Dr Wright was further concerned about an "unders and overs" approach where regional councils were allowed to degrade some waterways and compensate by improving others.