Manuherikia Catchment Group chairwoman Anna Gillespie said she was not surprised but was disappointed.
Not only was a six-year consent "not bankable", there were efficiency gains farmers wanted to invest in that were now also off the table.
She would not comment on what the decision meant for farmers in her group who had applied to replace their permits with consents.
The interim consents replace largely unlimited water-take permits that expire as the council writes new rules - the land and water plan - for water use around the region.
The court decision said the council's "plan change 7" had been substantially rewritten due to submissions, but the relief sought by many to allow for consents for periods of more than six years was not approved.
The decision said the court found the policies would likely reduce economic growth and potentially also growth in employment in the region.
It acknowledged the primary sector, in particular, was dealing with a lot and granting of consents for a short period added to the present state of uncertainty.
However, the six-year duration of consents was intended to discourage further investment in irrigation infrastructure and expansion of irrigated areas, it said.
And the six-year duration was linked to imminent change in policy settings.
The relief sought by many to either reject plan change 7 or to include provisions in it to allow for the granting of consents for up to 35 years, had its own risks.
"We acknowledge that, as a result of the changes to the plan change made by this decision, most, if not all, of the hundreds of permit holders who have already applied for resource consent in respect of expiring permits, will need to amend their applications if they wish to have the security of the applications being granted as a controlled activity."
Council chairman Andrew Noone said that the decision was a pivotal one for the future of water management in Otago, "especially given the weight of Te Mana o te Wai and the National Policy Statement for Freshwater Management 2020".
"We understand that the court's decision will not rest comfortably with some.
"It is now time for us to work together to achieve the expectations of the national policy framework for our communities and environment, and to look towards the future," Noone said.
Over the coming weeks, council staff would assess the implications of the court decision on resource consent applications that were being processed, and on future applications.
