Scientists trying to understand the rapid decline of freshwater crayfish in the Waikato River have secured almost $100,000 of funding from the Waikato River Authority.
Scientists from the National Institute of Water and Atmospheric Research (Niwa) will start a survey of the river's ailing freshwater crayfish, or koura, population early next year.
One of dozens of projects being funded by the authority, the survey will be used as a key indicator to gauge the river's health.
Niwa ecotoxicologist Sue Clearwater, who is leading the project, said the exact state of the koura population was unknown, but a limited pre-restoration survey of koura on the shores of Lakes Atiamuri and Ohakuri last year found none at all.
"We knew there was a lack of base-line information, and the survey suggested the situation is perhaps a lot worse than we thought."
The crustacean, which can grow up to 15 centimetres long, was found in tributaries, but all but absent from the main stem of the river.
Available information suggested koura were last present in the main river body in the mid-1990s, she said.
Scientists do not yet know what had caused the decline, but there were a range of possibilities.
A drop in water quality, predation by translocated eels or pest species such as catfish, and habitat loss could all play a part, she said.
"We think one of the reasons they may have declined is because of flow-ramping in the river, which is when the hydro companies rapidly change the levels of the river, sometimes twice daily."
Dr Clearwater said one of the big changes in the river since the mid-90s was the number of eels that had been transported upstream, creating an eel fishery where there was not one in the past.
"Eels are great predators of koura and the upstream koura populations were probably naive to having them around."
The survey will take place next year, focusing on some of the more inaccessible areas of the river from Huka Falls, through Lakes Aratiatia, Ohakuri and Atiamuri.
Scientists will dive various sites and conduct electric fishing surveys - where pulses of electricity are used to stun fish and invertebrates - in more hard-to-access tributaries.
Scientists will also use the traditional tau koura harvesting method - where bundles of bracken fern are sunk into the river bed and used to attract and harvest the crayfish.
River authority co-chairman Tuku Morgan said the state of koura was "one of those elements that gives us confidence that the river is healthy and thriving".
Mr Morgan said it was hugely important to restore the native habitats of koura, whitebait and freshwater mussels to ascertain whether current practices were harmful.
"They were an important part of our diet growing up.
"We used to catch them by the bucketloads, [but] it is now reserved for the memory bank."
Dr Clearwater said the information would be used in planning strategies.
"If we can clarify the causes for koura declining, we can start putting new management plans in place."
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