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The 3.7ha of land in Stone St is owned by the Otago Fish and Game Council and chief executive Niall Watson said on Saturday the council had agreed to let it be the site for the centre.
The property, including the council’s former fish hatchery, has a government valuation of $1.7 million.
The newly formed Lake Wanaka Trust plans to use part of the land for a new building containing laboratories, storage space and accommodation for field researchers, as well as educational facilities.
Mr Watson said there was no intention to develop the part of the property around the spring, which is the source of Bullock Creek, which runs through Wanaka.
"In terms of maintaining the quality of Bullock Creek, that area, which might be over 2ha, we think needs to be managed carefully."
In 1948, the government established a hatchery on the land next to the springs to raise trout and salmon for release.
The hatchery was transferred to Fish and Game in about 1990 and continued to be used for about 15 years until an alternative hatchery was established on the Taieri River at MacRaes Flat.
Mr Watson said the council was "really taken" with the idea of a research centre.
The effects of changes in climate and land use were two areas where more research was needed, he said.
Mr Watson said Fish and Game New Zealand had a "relatively modest amount of money" available for research.
Lake Wanaka Guardians chairman Don Robertson said money for the building would have to be raised, but scientists who used it would find their own research funding.
He hoped a management plan for Lake Wanaka could be produced that could be adapted for Lakes Wakatipu and Hawea.
"That’s something that should have been done decades ago."
Centre spokeswoman Maggie Lawton said the trust had signed a memorandum of understanding with Fish and Game and the University of Otago, which had committed to using the centre.
She said the next step for the trust was to begin raising money for the centre building.