Damning research into the populations of New Zealand's freshwater species indicate three-quarters are in decline.

Fresh water fish are on the decline due to habitat loss and pollution. Source: rnz.co.nz

The author said central and local government have failed to protect our native fish.

The research, published by Victoria University of Wellington, looked at 25 different fish species over the past 47 years.

Twenty of the fish studied as part of the research were natives and 15 of those were in decline. Thirteen native species showed significant declines.

Habitat loss and pollution have been named as the main drivers of this decline.

One of the authors of the report, Mike Joy said dams and irrigation in particular were having a negative affect, as it changed the natural hydrology of the riverbeds.

"The intensification that goes with the dams and irrigation means you have more nitrate and nutrients going into the systems, which means they get sicker and get algal growth, which leads to oxygen depletion and a whole raft of effects," Dr Joy said.

Dr Joy said the dams also blocked off migratory species of fish, leaving fish populations isolated and condemned to eventual extinction.

"We have these little populations we're protecting somewhere, but functionally they're gone and once they're gone from there, there's no replacement and we don't see them again," he said.

The report was conservative, and the problem was likely to be much worse, he said.

The report showed how badly central government and local government have protected fish and it should be treated as the canary in the coal mine, Dr Joy said.

"DOC [Department of Conservation] has failed badly in not protecting those freshwater fish, not doing anything about those barriers, despite having legislation that says you're not allowed to impede the passage of those fish, all they've done is come up with some guidelines."

Dr Joy said to top it off some of these endangered species were part of the whitebait catch and the longfin eel was commercially harvested.