Dentist Don Wallace contacted Fish and Game earlier this month after returning from the opening on the Greenstone where he found widespread didymo about 0.5km downstream of the McKellar Hut, on the true right of the river.
The didymo was also well established at the pool by the hut, Mr Wallace said.
The Greenstone Valley is near the Routeburn and was used by trampers and recreational anglers.
"Our interpretation is it's been put there by trampers washing their gear and washing in the river by the hut.
"We didn't check upstream towards Lake McKellar or the commercial walks.
"We don't believe, because of its location, that it has been put there by fishermen."
Mr Wallace told Fish and Game Otago chief executive Niall Watson it could spread into the rest of the Fiordland National Park from that point.
"Trampers often leave the Greenstone walk with wet gear and do a number of the walks like the Routeburn, Kepler and Milford track.
"Fishermen could also duck into the Eglinton on their way out of the Greenstone, if they have walked in from the divide."
Mr Wallace said he had done the opening on the upper Greenstone annually for 25 years.
"I've got to say that I myself, and my fishing mates who were with me on this trip, were devastated. We spoke to the wardens at the Howden Hut on the way through and they knew nothing of the didymo.
"In the last five years we have not seen a presence of a warden at the McKellar hut on opening weekend."
He said there were signs of didymo down the river, but it was around the McKellar Hut where it was most prolific.
"We can see establishment down the river in more prolific portions fuelled from this site.
"At the divide, there are signs and spray bottles targeting anglers but nothing is targeting trampers."
Mr Watson told the Otago Daily Times the presence of didymo in the back-country river was "a great shame" and "frustrating".
"It's a great shame that it's getting into the back country waterways, but it seems to be very difficult to stop the spread of it.
"Anglers are learning to live with it, but it's certainly not enhancing the experience for them.
"In Fiordland there are quite a number of rivers that aren't infected at this stage [but] it will be difficult to keep it out.
"Quite a large number of rivers are infected in Otago now, so the chance of keeping the ones without didymo-free is getting smaller and smaller really.
"It's really frustrating."
Mr Watson said there was no way to find the actual cause of the didymo spread, but recreational users not cleaning their equipment properly was "certainly a possibility".
"If they're going out into Fiordland, they need to recognise that a number of rivers in the Wakatipu area are contaminated with didymo and they need to clean their gear and equipment.
"People need to be aware of that, particularly if they're going from one river to another . . . [they] do have to be aware that didymo isn't everywhere yet and they should be cleaning and drying their gear to make sure that they're not spreading it."
