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Lindis Catchment Group filed the appeal against the Otago Regional Council's decision to restrict the summer flow of the Lindis River to 900 litres per second last week.
Those who submitted evidence during the Lindis River Catchment plan change hearing had until last Friday to appeal.
Farmers had hoped the minium flow rate would be set at 400 litres per second.
Committee member Bruce Jolly said the group was now ready for a long process.
The minimum flow placed on the Lindis River from the start of October to the end of May meant many farms would not be economically viable, Mr Jolly said.
Group members would pay the legal costs of the appeal proportional to how much water they used from the river for irrigation.
Now the appeal had been filed, Mr Jolly hoped the farmers could meet the regional council and find compromises. But if that failed they were prepared to go to the Environment Court.
Evidence from the plan change process would be revisited and the group would try to find new evidence to support their claims of the minium flow being set too high, he said.
At the time of the decision, farmers who relied on the Lindis River for the majority of their irrigation said if the flow rate remained they would have to walk away from their farms as they would no longer be able to make a living.
A spokesman for the Otago Regional Council said because the case was now before the court the council would not be making any comment.
Last month Fish and Game Otago said it would take part in any appeal process to ensure the summer flow limit remained at 900 litres per second.