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The study, expected to begin in the spring, will be carried out by Niwa.
It is being funded by grants from the Queenstown Lakes District Council, Otago Regional Council and the Department of Conservation.
The regional council's general manager of operations, Gavin Palmer, said the study would provide information about where wetlands could be reconstructed, and what each wetland would do to improve the quality of water flowing into the lake.
The Lake Hayes management strategy, adopted by the council in 1995, had the overall goal of improving water quality to a standard suitable for year-round recreation, and to prevent algal blooms, Dr Palmer said.
One of its strategies was to reduce flows of phosphorus into the lake.
"Wetlands work as sinks, and can regulate or trap the flow of nutrients, including phosphorus attached to sediment."
The study would also become the basis of an action plan to take to the community for consultation and implementation, he said.
Queenstown Lakes Mayor Jim Boult, a Lake Hayes resident, said he hoped it would be the "beginning of a new chapter" for the lake.