This month Judge Jon Jackson set a minimum flow for the river of 550 litres per second and a primary allocation of 1640 litres per second, which are the limits proposed by the Lindis Catchment Group.
This cancels the limits set by Otago Regional Council-appointed commissioners of a minimum flow of 900 litres per second and a primary allocation of 1200 litres per second.
Otago Fish & Game yesterday appealed the decision to the High Court, saying an error of law had been made.
The organisation backed the original limits set by the commissioners, saying they were better for the health of the river.
In its appeal the organisation said the court came to conclusions ''no reasonable decision maker exercising a decision-making power under the Act could have reached''.
It ignored the special protections applied to trout when it described them as an ''introduced pest'' which ''degrades indigenous ecosystems'', the group said.
It argued the court applied the wrong legal tests in several areas and its testing on the impacts on trout habitats was flawed.
The court could ''not reasonably'' have come to the conclusions it did in terms of lower minimum flows being better for the health of the ecosystems of invertebrates and fish species.
In a statement Otago Fish & Game chief executive Ian Hadland said the appeal was focused on seeking clarification on aspects of the judgement which had potential for national application.
He and other parties involved were unable to comment further as the decision was now before the court.
When the decision was made earlier this month it was welcomed by water catchment groups in Otago which said justice had been served.
