The 158ha reserve is where the Clutha River joins Lake Dunstan, and is near a proposed cycle trail.
Fish & Game has approved a budget of $3400 to remove mature willows, restore native plant species and create better habitat for waterfowl game birds, fish and native bird species.
The first 40 plants went in on Wednesday last week.
Fish & Game officer Ben Sowry said generations of families had enjoyed seasonal game hunting in the reserve.
"This is also a productive fishing area, and plans are afoot for a nearby cycle trail.
"Money collected from offences is used entirely to improve habitat in wetlands and other waterways," he said.
Funding comes from Fish & Game fines collected from fishing and hunting offences, but the council is also seeking partners to contribute more funding and labour.
Mr Sowry said willows had encroached on the island and channel areas, leading to a significant decline in open water that waterfowl used as loafing and feeding areas.
Willows were choking large areas of waterfowl habitat and removing them would also improve fishing in various channels, he said. Replacement trees included kanuka, kowhai, manuka, totara and cabbage trees. Flax was being planted to stabilise the river bank, and a variety of other species would also be planted.
