A leading freshwater ecologist says scientists have been vilified and ignored for speaking out while New Zealand's rivers and lakes have become more polluted.

He urged his fellow scientists to push for greater recognition of their science when it came to policy-making, and said if they didn't, they risked being a group that watched from the sidelines while the situation got worse.

Professor Russell Death, a freshwater ecologist at Massey University, gave a keynote address at the New Zealand Freshwater Science Society (NZFSS) conference in Nelson on Tuesday, where he received the Society's top prize for freshwater scientists.

In a candid speech, he told his fellow scientists that the pollution had happened "on our watch" and it was time for scientists to acknowledge they had played a role.

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"As a Society and as scientists, we really need to take some responsibility that this has happened on our watch," he said.

"It's happened over the last 20 years when the vast majority of us have been active freshwater scientists."

But Death also pointed to the difficulties that came with scientists speaking publicly about the issue, particularly for those reliant on funding from industries that may have a role in water pollution.

That group included scientists working for Crown Research Institutes, where primary industries could constitute a source of funding for research.

It also happened within universities, he said. He cited an incident earlier this year when his then-colleague, freshwater ecologist Dr Mike Joy, was taken to arbitration by Massey University over Joy's public criticism of the Environmental Protection Authority's (EPA) then chief scientist, Dr Jacqueline Rowarth.

Ironically, just months earlier Joy received the national Critic and Conscience of Society award which acknowledges academics who use their expertise to raise public awareness of issues.

He was not formally punished by the university, but has since left. Rowarth also left the EPA.

WARWICK SMITH/STUFF Freshwater ecologist Dr Mike Joy, who was taken to arbitration by Massey University over public criticism of another scientist.

"There are very strong disincentives for speaking out," Death said.

"For those of us who do speak out, our funding is clearly impacted, and we don't get as much funding as we would get [if we didn't] speak out about various industry bodies in New Zealand.

"We do have to speak out, and we are allowed to speak out, but we speak out at our peril and our cost."

In his address, Death said New Zealand's water quality was not "something to be overly proud about," citing its rate of endangered native freshwater species – which was the highest in the world – and its rate of waterborne disease, which was among the highest in the western world.

He also cited deaths related to contaminated drinking water, as seen in the Havelock North disaster in 2016, in which an outbreak of gastroenteritis in the public water supply made thousands sick and was linked to at least four deaths.

"I really thought that once people started dying that things would change and people would take notice, however, that doesn't seem to be the case," Death said.

"It still seems to me that water quality is not improving. If it is, it's only very, very slowly improving. To my mind, there's no convincing evidence that we've turned around the decline that's been going on over the last 20 years."

The Labour-led Government is working on a new freshwater quality framework, which would replace the one instituted by the former National Government in 2013, which was updated in 2017.

The updated standards were criticised by many freshwater scientists, including the NZFSS itself, which said it was concerned by the "widespread decline in aquatic biodiversity and water quality in New Zealand."

The standards would not apply at all to around 90 per cent of rivers, it said, and the swimmability guidelines were more lax than those it was replacing.

New Zealand's freshwater scientists had done valuable, at times world-leading research, Death said, but scientists – as well as the Society itself, for which he had been a member for 30 years – needed to stand up and push aggressively for their science to be practically applied.

"I think we really do need to do better," Death said. "We are the expert body of freshwater science in New Zealand, and we are the people that can have an effect.

"I like to think we could be a little more supportive of those of us who speak out. I think Mike Joy in particular has been vilified for speaking out – a lot of us congratulate him for doing it because we're scared to do it ourselves.

"We need to do more than just meet every year, talk about how bad things are and go 'yup, we really should do something' and then carry on and essentially not do anything... I hope we don't end up being a society where we just record the decline in water quality, the loss of our native species, and how bad that things have got."

The Minister for the Environment, David Parker, will speak at the conference on Thursday to update scientists on the progress of the new water quality rules.

He has previously said the new policies would be in place by 2020, and would include rules around a wider range of contaminants than the existing standards. They would likely include stricter rules around intensive farming, as well as a way for councils to more easily review resource consents, and greater collaboration with Māori.

This week's NZFSS conference was its 50th, and has drawn its largest attendance ever. It has had a strong focus on mātauranga Māori, and incorporating Māori values and expertise into freshwater management.