One of the South Island's top trout fisheries, the Hurunui River in north Canterbury, has fallen victim to the invasive "rocksnot" algae.
Biosecurity NZ said that the didymosphenia geminata pest has been found in the upper river - the North Branch Hurunui, about 7km downstream of Lake Sumner.
The organism is likely to be present in Lake Sumner, and to spread down river.
The Hurunui is a medium-sized braided river regarded as an excellent trout fishery along its entire length, and a good salmon fishery which is often clear and fishable when the major rivers to the south are in flood.
"This is hugely disappointing news for this highly valued river," Canterbury regional council deputy chairman Robert Johnston said.
"All we can do is to urge people to keep up the clean, dry and disinfect routines and see if we are able to keep this organism out of other waterways."
Rocksnot has been confirmed in many South Island rivers, including the Waitaki, despite biosecurity officials urging anglers and other river users to clean vehicles, clothing and equipment to avoid transferring the microscopic algae to the remaining un-infested waterways.
