The Department of Conservation says the focus has turned to stopping an invasive freshwater algae from spreading further around Fiordland.
A water sample has confirmed the algae has passed over the west divide to Large Burn Valley, which drains into Caswell Sound, south of Milford Sound.
Didymo was first reported in New Zealand in the Waiau River in Southland in 2004, and the discovery in Fiordland is the first time it has been detected in a river west of the divide.
DOC freshwater ranger Lyndsay Wilson told Radio New Zealand's Morning Report programme didymo is impossible to get rid of it, so people need to know what to do to stop it going further.
Mr Wilson said recreational boat users must clean and dry equipment. He said washing gear in detergent solution will kill the alage.
A review of the didymo controls in the region is under way.