Authorities in charge of the country's rivers have been drastically underestimating how much water trout and salmon need to grow and thrive, a study says.

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The Cawthron Institute study found flow levels in rivers were almost twice as low as they should be, and too much water was being syphoned off for farm irrigation.

The institute's lead researcher for the study, John Hayes, said the old model regional councils had used until now had not acknowledged the relationship between fast-flowing rivers and the number of invertebrates, such as mayflies, they supported.

The faster the river, the greater the chances the insects eaten by trout and other fish would be dislodged from the river bed - and make their way up to the surface, where the fish feed.

"The traditional model seems to be underestimating the flow requirements of the fish relative to the new model - substantially underestimating them, by almost double - so it has some pretty significant consequences."

The Southland and Otago Regional Councils were already using the study's findings when assessing how much water they allowed farmers to take for irrigation, and Dr Hayes said he expected other councils would follow suit.

"This new model will drive a paradigm change in the way that minimum flows are assessed for trout and salmon in New Zealand and throughout the world," he said.

Fishers notice decline in stock

Fish and Game Southland manager Zane Moss said anglers had noticed a steady decline in fish stocks and size at the same time as farmers took more water from rivers for irrigation.

He said the research showed trout and salmon had been sold short by the model councils were using.

While dairy farming contributed a lot to the economy, so did game fishing, he said.

"Trout fishing is incredibly important to New Zealand culturally and from tourism as well, there's hundreds of millions of dollars of tourism associated with trout fishing."

The researchers said their findings would have major implications for Canterbury, where more water was taken for irrigation than anywhere else in the country.

Nobody from Canterbury Regional Council was available to comment.