Central Otago's Manuherekia catchment has been given a funding boost to clean up the waterway.

Environment Minister David Parker today said it would be the third catchment area to benefit from the At-Risk Catchment programme - which provides $12 million over four years nationally.

The money would initially be used to install fencing, restore wetlands in Thomson's Creek, assess fish levels and address concerns over native species.

Earlier this year, Otago Fish & Game Council said a report into water quality in the catchment made for sobering reading.

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The report, which focused on water quality issues from the past 10 years, was presented at a meeting of the council in Roxburgh in July.

Parker described it as a popular place for recreation activities as well as a source of water for farming, viticulture and horticulture.

"However, the river is under pressure, with water quality declining and over-allocation of water reducing the minimum flow needed for ecological processes, such as providing habitat for wildlife, and for recreational use."

"We will work with farmers and others in the community to help understand what can make the greatest difference and then what interventions to take.

"The lessons learned from 'exemplar' catchments like Manuherekia can then be passed on to others."

A second project would follow to further improve water quality in the area.

The At-Risk Catchment programme has also announced funding for Te Hoiere/Pelorus in Canterbury and Kaipara Moana in the North Island.