As University of Canberra Centre for Applied Water Science director, the Otago graduate has worked on diverse freshwater issues in Australia, including river restoration, climate change, impacts of pollutants, effects of forestry and farming, and native fish biology.
He has also been active in working with indigenous groups to integrate cultural knowledge and practice into river management.
Prof Thompson was "thrilled" with the position and the opportunities it brought.
"I look forward to building on Dame Carolyn’s research legacy, and the broader freshwater research legacy at Otago, to make a real difference to New Zealand’s freshwater environments."
There would be a lot for him to learn in his first year, he said.
His initial focus would be on "talking to people in industry, community, government and the research sector, to understand the current state-of-play".
"This role really gives me the freedom to contribute to real improvement in the condition of freshwaters in New Zealand, particularly in the South Island."
Intensification of farming and forestry, urban sprawl and a changing climate were all realities of the world we live in.
"My research is about how can we accommodate the demands of society, but also do our best to ensure that our freshwater environments are protected and restored."
Dame Carolyn is a University of Otago emeritus professor and leading international authority on the ecology of lakes.
She had a long association with the university, beginning in 1969 as a zoology lecturer before becoming head of the department from 1998-2005.
The idea behind establishing the new chair was to provide and develop both research and leadership in the area of freshwater sciences, and by doing so help to maintain, enhance and protect freshwater ecosystems into the future, she said.
"His appointment to the position will strengthen Otago University’s research, teaching and training in freshwater sciences and management."
Prof Thompson will begin the role in January.
