Otago Regional Council has backed recommendations to ensure Lindis River still flows in the summer months.
A minimum flow of 900 litres per second be will be set for the river between October and May beginning 2021 as part of a wider plan that considers water allocation in the area.
The council's policy and resource planning director, Fraser McRae, said the river historically dried out over summer months because of heavy extraction by farmers for irrigation.
He said because of historical mining privileges the river had been over-allocated for irrigation, which damaged fish spawning and movement.
Those privileges still allowed for the bulk of the water to be extracted and do not end until 2021, he said.
Restoring water flow to the area would protect the ecosystem and encourage sustainable management of the river's resources, Mr McRae said.
"It's very detailed, it's very technical but at the back of [it] is trying to improve the aquatic habitat for all the values that [it] produces in the area.
"We've got to give farmers time to make the adjustments needed," he said.
The council said it acknowledged the changes were likely to have an economic impact on farmers in the region, as many would have to look elsewhere for their water supply and compete with other water users during the low-flow period of summer.
However, Mr McRae said those costs would eventually be offset by converting to more efficient irrigation infrastructure and creating better water storage.
"This policy is attempting to say to people, if you have an alternative source, then you should use that so that those people who, this is their only source of water, have better access."
Other water sources like an underground aquifer or Clutha river would be good alternatives, he said.
Some farmers had already created bores and put in central pivot irrigators to remove themselves from consequences of the plan change, Mr McRae said.
The council said it would increase the primary allocation limit from 1000 litres per second to 1200 for those farmers who had no other option than to extract water from Lindis River.
The changes will occur in 2021, which is when the Resource Management Act's directive to phase out the old mining privileges comes into effect.