The invasive algae didymo has been found in the West Coast's internationally renowned trout fishing Karamea River.
The Department of Conservation said today the discovery of the weed in the river at the heart of the Kahurangi National Park was a "serious concern".
DOC Motueka area manager Martin Rodd said it would impact on the "significant natural values" of the river and would be detrimental to the outstanding recreational fishing the Karamea offered.
"The Karamea-Leslie Track, which runs alongside the river, also is a popular backcountry tramping route."
If the didymo spread further in the national park it could also affect rivers managed as important habitat for the endangered native whio or blue duck.
The algae was discovered by a fishing guide at a site between Moonstone Lake and Venus Hut.
Mr Rodd urged anyone visiting the area to thoroughly clean and dry their fishing gear or tramping boots before entering another river.
The invasive, smothering algae, also known as "rocksnot", has spread quickly throughout South Island rivers since it was first discovered in 2004.