Last month the Department of Conservation, with help from Fish and Game and the Clutha Fisheries Trust, caught nearly 200 goldfish from ponds in the Albert Town wetlands.
The fish have long been established in the wetland's artificial ponds. What concerns Doc is the population in the nearby Albert Town Lagoon.
Doc Wanaka ranger Paul Hondelink said water from the lagoon flowed into the Clutha River, so the goldfish there posed a greater environmental risk.
It was relatively easy to remove the fish from the artificial ponds using an electric stun device and nets but the lagoon was a different story, Mr Hondelink said.
Because of its depth and plant life Doc was unable to use the same method.
Mr Hondelink was trying to find a way to stop the fish spreading into the river and downstream into Lake Dunstan.
''It's something we need to get outside advice on and I have already been in contact with an expert about the issue, so we will see where it goes from there.''
The bottom-grazing fish ate native plants, damaging already fragile ecosystems and burrowed into mud, which affected water quality, he said.
White herons did a good job of keeping the lagoon's goldfish population under control but there were not enough birds for that to be sustainable, he said.
The goldfish found a home in the ponds after they were dumped illegally, Mr Hondelink said.
Signs were being made which would hopefully stop people disposing of unwanted fish in the ponds and lagoon, he said.
It is an offence to dump aquatic life into fresh water under the Conservation Act and anyone caught doing so can be fined up to $5000.
