ORC chairman Stephen Woodhead said the outcome was something everyone involved could be proud of, particularly the local community, which had constructively contributed to it.
Otago Fish and Game Council environmental officer Peter Wilson said the plan change was a "positive outcome'' after a "good process''.
This was the last of the main South Otago rivers "under pressure'' to be included in minimum-flow and water-allocation arrangements, though some other waterways there might be included in future.
And it was "always good to resolve these things'' by mutual agreement rather than by court decision, he said.
The Waiwera is a tributary of the Clutha River and is located inland from Balclutha.
Four farmers are taking water from the river for irrigation and stock.
The Waiwera River plan change also includes water allocation limits and a monitoring site for the river.
ORC director policy planning and resource management Fraser McRae said the plan change provided certainty for the community, which relied on the river for recreation, cultural and agricultural uses.
Minimum flows were "the level below which no more water can be taken, to protect the values of the river'', he said.
Plan Change 3C was publicly notified in December 2014 and submissions on the change were heard in April last year.
In August, the ORC hearing committee notified its decision on a minimum flow of 300 litres per second (300l/s), and two appeals were later made to the Environment Court.
These appeals were resolved through mediation last December, resulting in an agreed minimum flow of 280l/s.
This plan change takes effect on March 1.
And a "recovery flow'' provision means that if the flow drops below 280l/s because of consented water taking, it must return to 310l/s before taking can start again.
Farmer Phil Neame, who runs 500 cows on a nearby farm and draws water from the river, took an appeal to the Environment Court over the proposed 300-litre level, which he had regarded as too high.
He said his submission, involving PJ and AM Neame Ltd, had been supported by science.
And he was pleased with the outcome, and that matters had been resolved amicably, through mediation.
Mr Wilson said Fish and Game Otago had taken the other court appeal, supporting a minimum flow of above 260l/s.
