"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."
Co-author Dr Emily Elston said New Zealand could implement some "real changes" which would "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".
"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 Government has set out core priorities and objectives to improve freshwater management in the new National Policy Statement (NPS) for Freshwater Management.
This introduced new minimum or "bottom line" requirements that must be achieved so the water quality was suitable for ecosystem and human health, and included a range of other actions for regional councils.
The authors argued the NPS 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.
However, a Ministry for the Environment spokesperson said three of the six identified priorities had been addressed in part in the NPS, which was being expanded.
The additions would address sediment for lakes and rivers, and consider what attributes were appropriate for wetlands.
What other scientists say
Dr John Quinn, the National Institute for Water and Atmosphere's chief scientist for freshwater and estuaries, agreed with the "broad direction" of the proposed priorities and was optimistic that work around the NPS would advance some of them.
"It's when we start looking at how we can get there that things get more challenging," he said.
"Knowledge about critical habitats is crucial to successful action to enhance biodiversity, but we still have many important knowledge gaps that policy will have to deal with."
Dr Quinn pointed out it had only been in the last two years that NIWA researchers had identified the critical spawning habitats of two of our largest freshwater native fish, lamprey and giant kokopu.
Professor Jenny Webster-Brown, director of the Waterways Centre for Freshwater Management run by University of Canterbury and Lincoln University, felt the National National Objectives Framework would go "some way" to reaching the priorities, but she added this was a work in progress.
"Even if all currently confirmed actions of the NOF could be implemented immediately, it would still be many years before inevitable weaknesses and inadequacies come to light through the monitoring data, and can be addressed through revision of the framework."
That said, more needed to be done right now to actively protect our aquatic ecosystems, and reports like this helped "to keep our eye on the ball" she told the Herald.
"It reaffirms that unless we actively take steps to protect all interconnected parts of the freshwater environment, from all of the activities that threaten native and endemic species in this environment, we will lose many more of these species."
President of the New Zealand Freshwater Sciences Society, Professor David Hamilton of Waikato University, said while the information in the report was "not especially new" - the decline of freshwater quality and biodiversity had been known for some time - the synthesis in the document was useful.
"The report is also useful in identifying aspects of freshwater that New Zealanders value - the fauna and flora - and going beyond the generic term 'water quality' when describing recent declines in freshwater systems in New Zealand."
However, Dr Hamilton made several criticisms about the report.
The Parliamentary Commissioner for the Environment had already identified how land use and nutrient pollution affect water quality, Dr Hamilton said, but did not make any comment about guidelines to protect freshwater biodiversity, as claimed in the report.
He pointed out how the report recommended the protection of habitat critical to the survival of New Zealand's freshwater species, notably river habitat to protect ecosystem health in the National Objectives Framework.
"In fact the Resource Management Act (1991) included provision for the preservation of the natural character of rivers and their margins," he said.
"What has not occurred is a consistent approach by councils to protect these habitats under the powers vested in them under the RMA.
"In this respect the report has correctly identified that river habitat should be a critical area of concern in the next iteration of the National Objectives Framework, so that there is a consistent approach to protection of rivers at the national scale."
While the report discussed the establishment of monitoring and recovery plans for New Zealand's threatened freshwater invertebrate fauna, it provided no guidance as to what the recovery plans should entail, he said.
Commenting on the final priority flagged in the report - the need to establish wide riparian zones that connect across entire catchments - reflected the need to create freshwater biodiversity corridors and connect these across different ecosystem types such as groundwater aquifers and wetlands, he said.
"The current situation in New Zealand is characterised by major time and economic investments in riparian planting and retirement being made by government, community groups and other stakeholders at local level, but with limited overview and synthesis to evaluate their effectiveness at a catchment scale.
"The National Science Challenges, such as New Zealand's Biological Heritage and Our Land and Water, need to provide underpinning research and synthesis to ensure that these efforts represent best value for money and support whole-of-system restoration."
