The rock-lined ponds date from 1868 and were built by the Otago Acclimatisation Society, the forerunner of the Otago Fish and Game Council.
''These are the birthplace of where brown trout in New Zealand were introduced,'' Fish and Game Otago chief executive Niall Watson said.
They were rediscovered by Mountain Bike Otago club members in 2011, when they were building a new track up the Opoho Creek valley.
New Zealand Historic Places Trust regional archaeologist Dr Matthew Schmidt and a team of volunteers spent International Archaeology Day on Saturday uncovering the ponds.
''They're now clearly visible.''
It was from eggs transported from Tasmania, and hatched in the ponds, that the region's rivers, including the internationally recognised brown trout fishery of the Mataura River, were stocked with brown trout.
Dr Schmidt said the stone-lined ponds were in really good condition for their age and illustrated an important part of the city's social history.
''They tell a lot about Dunedin at that time, as the acclimatisation societies were formed to provide food for the common man. Back in England, you had to pay to sports-fish.''
The group had been able to remove the vegetation around the ponds ''sensitively'' so the stone work remained in place. The lower pond still held water.
''You can see all the features. It's very cool.''
Mr Watson said the council believed the future management of the ponds was important and provided the public with an opportunity to reflect on the city's colonial past.
''I'd have to say that brown trout were one of the more successful introductions. When you look at this site, consider the materials they had to work with and logistics of transferring live trout eggs from Tasmania, it's a marvel that they achieved what they did here.
That tenacity is what makes this such a special site,'' Mr Watson said.
In a joint project with the mountain bike club, the Historic Places Trust and Fish and Game, a small fence and an interpretation panel would be installed, hopefully in time for the Otago Acclimatisation Society 150th anniversary celebrations next year.
