Cardrona Valley residents and farmers say the proposed minimum flow levels the Otago Regional Council wants imposed to regulate the Cardrona River will affect upstream water users.
The ORC wants to prescribe minimum water flow levels for the river during the dry summer season.
However, the dry months of February until April coincide with a period when farming and crop-growing demands for irrigation are at their peak.
Cardrona Valley Community Association chairman John Scurr has told residents meetings have been scheduled with the ORC for farmers and water-users to discuss their concerns.
ORC staff completed a hydrology report on Cardrona River flows recently, which highlights how the waterway can run dry during peak times in the summer.
The report says water races, which draw from the river near a section of the valley known as the Larches, affect flow levels downstream before the Cardrona confluence with the Clutha River.
"The diversion [of] river water into races in the vicinity of the Larches has a major influence on the past and present-day groundwater recharge and habitat condition of the lower catchment," the report said.
Water races used to harvest water for the dry months when irrigation water is required had resulted in two "observed" incidents when the Cardrona River had run dry in 2009 and 2010, the report says.
Cardrona Valley association deputy chairman Ben Gordon, who farms Avalon Station near the Cardrona township, said the river flowed underground before it resurfaced near the confluence.
While a section of the Cardrona River appeared to be dry during summer months, it ran through and under the gravel riverbed, to resurface.
Waiorau Station owner John Lee agreed with Mr Gordon and said the Cardrona River had "always" looked like it dried up in the summer.
"Historic" hydrology tests had shown underground water flow measurements for the Cardrona River were similar to upstream levels, he said.
The ORC wants to site a permanent flow station at the confluence of the Cardrona and Clutha Rivers "because it is crucial to the implementation of the proposed management flows", the report said.
The report recommends the results from a computer modelling river flow programme be used to set a minimum flow level.
ORC staff should consult Cardrona Valley residents before any flow levels are prescribed, the report recommends.
