Mr Innes established and runs Healthy Harbour Watchers, a group of secondary school pupils trying to plug the information gap about Otago Harbour.
The group grew out of research he carried out while on a Royal Society fellowship in 2005, when he realised there was no readily accessible information on the quality of the harbour's water.
Mr Innes said he was surprised by the acknowledgement.
"The stuff I have achieved has been because I had opportunities to meet quite a lot of people through my fellowship. I was good at persuading people to help me and also quite good at picking talent from schools to be part of projects.''
The awards, presented at the New Zealand International Science Festival, acknowledged those who had contributed to science in Otago, festival director Chris Green said.
"They are the unsung heroes of our daily lives who bring science to life and remind us through their actions to stay curious and to look for answers to many of the issues facing us today,'' he said.
The other award winners were: Charlotte Steel (student); Ann Cronin (non-profit/community; Bianca Sawyer (post-graduate student); Amadeo Enriquez-Ballestero (science communicator/teacher); Andrew Innes (sustainability); Peter Fennessy (business).