New Zealand's freshwater fish species are in peril - and especially in our pastoral countryside, researchers say.

In a study published today, Victoria University's Dr Mike Joy and colleagues compared land use changes and more than 20,000 freshwater fish records since 1970.

The data, which covered fish distribution and abundance trends, along with a key measure of water pollution called the Index of Biotic Integrity (IBI), showed more than three quarters of 25 analysed species were in decline.

About the same rate of decline was found in 20 native fish species - and in two thirds of cases, the drop was a significant one.

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Further, the study found more species were in decline around land dominated by pasture compared with areas covered with natural vegetation - a trend also shown among the IBI data.

That declines were worse in pasture catchments than those characterised by scrub or forest wasn't surprising, Joy said, although the rate of decline was nonetheless "scary".

In pastoral areas particularly, some of the most striking falls were observed among longfin eel and common bully.

Across all land types, the biggest drops were also recorded among redfin and bluegill bully, lamprey, brown trout, shortjaw and giant kokopu, black flounder and torrentfish.

Joy pointed out that it wasn't until the early 1990s that New Zealand assessed the threat status of its native freshwater fish, finding that one in five were either threatened or at risk.

It was an "appalling figure", he said, but also now old news - the current proportion was 74 per cent.

Globally, the average was just 37 per cent.

The giant kokopu was among native freshwater species that have experienced big declines over past decades. Photo / Auckland Council
The giant kokopu was among native freshwater species that have experienced big declines over past decades. Photo / Auckland Council

"We've gone from one species out of every five being in trouble to a situation where three species out of four are staring extinction in the face, and we've done it in one generation."

Given the study's findings, he said, it was "bizarre" that there was little protection for native fish.

"And the fact that despite these declines and developed world's worst proportion of threatened species we harvest them, the Department of Conservation [DoC] doesn't protect them."

Joy acknowledged a just-announced amendment to the Conservation Act aimed at native freshwater fish, but added this only covered protected areas.

"They have to get there first, through the polluted unprotected rivers."

He was also sceptical of new guidelines around structures built in rivers and streams that could impede migrating fish, criticising them as guidelines only.

"Under the Freshwater Fisheries Act 1983, it is clearly stated it is illegal to block native fish passage - but there have been thousands of barriers put in since then and DoC has to my knowledge never used their powers under this act to do anything."

"We've been trying to have our cake and eat it - we need to stop or soon there won't even be crumbs left," Victoria University's Dr Mike Joy says. Photo / File

Tackling the decline of fish, he argued, could only be done by addressing wider issues facing our rivers, streams and lakes.

"We need to match land use to soil types and slopes to control runoff, we need major reductions in intensity, and we need to look hard at the way local councils are charged with protecting both the economy and the environment when they apply the Resource Management Act - and yet somehow always end up letting the economy win," he said.

"We've been trying to have our cake and eat it. We need to stop or soon there won't even be crumbs left."

The Government was working on new bottom-line rules for regional councils that would remove farming intensity as a "permitted activity" and set tougher levels for nutrients.