Details of the two days of mediation are confidential, but the aim of the exercise was to thoroughly explore the differences and agreement between the parties, Otago Fish and Game chief executive Niall Watson said.
The New Zealand and Otago Fish and Game Councils had sought an amendment of the water conservation order on the Nevis so damming or diversion of the river was banned.
The application drew 248 submissions and was heard by a special tribunal appointed by the Ministry for the Environment.
The tribunal's recommendation, announced in August, was in favour of the conservation order being changed.
It found the river had one outstanding characteristic that was not protected by the original conservation order: the presence of a native fish called Gollum galaxiid, a species found only in the Nevis River. A ban on damming or diverting the river was vital to protect the habitat of that native fish, it said.
The tribunal's finding was challenged by three submitters - Pioneer Generation, the fish and game councils and Whitewater New Zealand - and now the matter will be heard by the Environment Court.
Pioneer, a power company with plans for hydro-electric development on the river, has opposed the tribunal's recommendation.
The councils asked for the river's wild and scenic landscape and trout fishery values also to be recognised as "outstanding" when the matter is reconsidered. Whitewater New Zealand, a recreational kayaking group, wanted protection of the "nationally outstanding" whitewater kayaking amenity provided by the river.
No date has been set yet for the matter to be heard in the Environment Court.
