Only a few thousand of the ducks - also known as whio - are left in the mountain torrents where they live.
Amy Whitehead is this year's overall runner-up in the latest MacDiarmid Young Scientist of the Year Awards, announced last night.
A conservation ecologist, Ms Whitehead (30) gained a BSc (hons) degree in ecology and zoology from the university in 2001.
She also won the Understanding Planet Earth category in the awards, presented each year by the Foundation for Research, Science and Technology.
"I'm really excited.
"It's great to be recognised in that way," she said. "One of the things that defines us as New Zealanders is our natural history.
It's a big part of our identity, so we need to make sure we don't lose any of our threatened species."
Born in Wyndham, Southland, she grew up in Te Anau, and attended Fiordland College.
As overall runner-up, she receives a cash prize of $5000 and a travel grant to attend a science event in Australia or New Zealand.
She receives another $5000 as a category winner.
After completing her Otago degree, she gained an MSc from the University of Georgia, in the United States, and recently submitted her PhD thesis at the University of Canterbury.
John Watt (27), a PhD student at Victoria University of Wellington, whose research could result in a cheap and effective way of removing toxic pollutants from vehicle emissions, was named the 2009 MacDiarmid Young Scientist of the Year.
His win gives him a cash prize of $10,000, a further $5000 as an award category winner, and a trip to an international science event, as well as the MacDiarmid medal.
Otago University MSc physiology researcher Mickey (Jui-Lin) Fan (24) won the $5000 national masters level research award, sponsored by the Royal Society of New Zealand.
He won the award with innovative research making use of high-altitude conditions at the Pyramid Research Laboratory in the Himalayas.
He was investigating sleep apnoea, which causes some people to stop breathing when they are asleep.
Foundation officials said that Mr Fan's research held promise for reducing the risk of heart attack, stroke and sudden death in people with heart conditions.
Born in Taiwan, he attended Wakatipu High School. - Additional reporting NZPA
