The Selwyn River's flow has dipped 60 per cent in eight years, with low levels contributing to a dwindling trout population, a report says.

The man behind the report said irrigation shot up by 60 per cent between 2008 to 2015, and Environment Canterbury (ECan) confirmed there was a correlation between irrigation take and water flow levels.

Federated Farmers said dwindling trout numbers could be down to a number of factors though.

RICHARD COSGROVE/FISH AND GAME NZ Fish and Game field officer Steve Terry releases fish rescued from the Ashley River further downstream into the Waikuku Stream, a tributary of the Ashley.

Consulting engineer and longtime Lake Ellesmere fisherman Alan Strong produced the report, which used ECan's science and the latest state of the lake report.

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The collapse of the Ellesmere/Selwyn fishery was illustrated by Coes Ford, where in 1964 Fish and Game trapped 14,000 trout moving up the Selwyn River to spawn. In 1984, in the same position, just 40 trout were trapped.

RICHARD COSGROVE/FISH AND GAME NZ North Canterbury Fish and Game staff rescue fish trapped in pools on the rapidly drying Ashley River near Rangiora. Ryton Barr places trout fingerlings into the holding tank where they await release further downstream.

Trout numbers had never recovered to previous levels.

Strong found that since the 1970s, water taken from rivers and aquifers directly below the ground had increased drastically, which corresponded with a decrease in lowland river and stream flows.

In 1998, the weekly mean average low flow (MALF) for the Selwyn River at Coes Ford was 700 litres per second. By 2006, it had dropped to 280 litres per second.

JOSEPH JOHNSON/FAIRFAX NZ The Selwyn River, 2 kilometres from the river mouth at Lake Ellesmere, near Selwyn Huts.

"This is a 60 per cent drop in river MALF flow when irrigation take went up by 60 per cent," Strong said.

In the week of March 6, the flow at Coes Ford was 80 litres per second, which Strong said was not enough to support a viable trout population in the river.

He attributed the trout population collapse to several factors, including pollution, lake level control, loss of spawning areas and over-fishing.

"It is a complex issue, but [irrigation is] a big part of it. We need to do it, but we need to be smarter about it," Strong said.

Federated Farmers' water and environment spokesman Chris Allen said there could be "many causes" as to why trout population was dwindling.

ECan acting surface water science manager Helen Shaw said abstraction of both ground and surface water had contributed to lower water flows in the Selwyn River, which was over and above what could be expected from climatic variation.

The lower flows had increased the extent of drying along the river, restricting the ability of trout to reach spawning grounds.

Shaw said declines in the health of Lake Ellesmere and its other tributaries were also likely to have reduced overall trout numbers.

"It is also possible that the historical numbers and size of trout were never sustainable over the long term," she said.

"The heyday of the Selwyn River trout fishery may have occurred when trout had only recently been introduced and had capitalised on a bonanza of food resources which were not adapted to trout predation."

Meanwhile, low water levels and environmental degradation were forcing Fish & Game to salvage fish from Canterbury's rapidly drying rivers.

Authorities had rescued fish from the Ashley River for the past four years, but never at this time of year.

Officers patrolled the Ashley River, near Rangiora, on Monday, rescued 30 trout and 20 eels from the Ashley River, near Rangiora, on Monday, and took them to the nearby Waikuku Stream, where water levels were healthier.

Fish & Game officer Tony Hawker said there was "no doubt" it was a dry year, but irrigation was also to blame.

"What fish are left, we are trying to protect them by restricting the winter fishing, and protecting those spawning sites."