The mystery of what caused New Zealand's only known extinction of a native freshwater fish has been solved, with scientists blaming the upokororo's demise on humans.

Further, they say their just-published findings hold important implications for those species left in our waterways.

The silver-coloured fish, which grew to nearly 50cm in length and was also known as the NZ grayling, was once abundant in the country's rivers and streams.

Still common in 1860, by the early 1900s the fish were being reported as scarce, with the last-ever catch recorded in 1923 – an ecologically rapid loss.

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The species was given legal protection – but only after it became extinct – and scientists have long been trying to understand what brought about its end.

Now a new study has shown the missing piece of the puzzle may have been poor water quality and degraded habitat due to human activity around the time of European settlement.

Up to now it was widely assumed habitat degradation, over-fishing and the introduction of trout, a key predator of larvae and juvenile upokororo, were the three drivers.

Because upokororo were a shoaling species, and numbered into the tens of thousands if not millions, they were easy prey for fishers who killed them in the thousands, often chasing them into a confined space and scooping them up in nets.

So abundant were they, they were used as fertiliser on market gardens.

But habitat degradation, fishing and predation by trout couldn't fully explain the speed of upokororo's disappearance, or the fact they disappeared from isolated pristine rivers.

After examining hundreds of historic records and using modern data modelling techniques, PhD candidate Finn Lee and Professor George Perry, both of the University of Auckland's School of Environment, concluded that another factor may have been the nail in the coffin.

That was the species dispersal strategy.

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Upokororo were amphidromous – they migrated from river to sea and back at some point in the life cycle - but unlike salmon, it's believed they did not instinctively return to the place they were born.

This meant they returned to breed in rivers and streams of poor water quality or inhabited by trout and this in turn led to what ecologists call population "sinks".

Sinks was the term is used to explain a "sinking lid" ecological theory whereby once-healthy populations do not reproduce at a rate high enough to establish sub-populations and so populations slowly "sinks".

Still common in 1860, by the early 1900s, upokororo were being reported as scarce with the last-ever catch recorded in 1923 - an ecologically-rapid loss. Photo / J Buchanan
Still common in 1860, by the early 1900s, upokororo were being reported as scarce with the last-ever catch recorded in 1923 - an ecologically-rapid loss. Photo / J Buchanan

"Our modelling shows these population 'sinks' could be the vital missing link," Lee said.

"We factored in over-fishing and predation by trout and while those things made a big difference, once we factored in dispersal among rivers and lower breeding rates from poorer quality habitat, then it clearly showed how the fish became extinct so fast."

The researchers say the study had significant implications for other freshwater fish, more than 70 per cent of which are at risk for under threat of extinction.

In particular, there were concerns over whitebait, and whether current restrictions are enough to protect them.

Like other countries, New Zealand faced big challenges to protect its freshwater species, but for history not to repeat itself, Perry said, we needed to know what happened in the past.

"Globally freshwater ecosystems are under immense strain, facing habitat loss, invasive species, climate change and over-exploitation, so understanding what happened in the past might allow us to stop extinctions of freshwater biota in future."

The Australian grayling was closely related to upokororo and listed as a vulnerable species under Australian environmental law.