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ORC environmental monitoring director Jeff Donaldson said despite surrounding rivers, including the Motatapu, Shotover and Kawarau, testing positive for the micro organism, also known as rock snot, it had been hoped its spread into the Arrow River could be stopped.
The positive test at The Hills indicated didymo was present in the Arrow irrigation scheme used to irrigate Sir Michael Hill's championship golf course, but that did not necessarily mean it was also in the river.
The Hills superintendent Brendan Allen said the irrigation system began blocking last summer and a sample was sent to Niwa for testing, which found ''traces of didymo''.
The water race feeding the irrigation scheme is located just below Macetown.
At the golf course the freshwater algae had clung to rocks, which had created additional work for The Hills staff who had cleaned The Canyons water feature, near the 17th hole, several times over summer, while the bottom of the water race appeared to be ''slimier''.
''It's not ideal, but we have found ways of dealing with it.
''Our waterways are not used by people swimming or fishing. It's far more significant for recreational users and river users than for us.''
When contacted by the ODT, Mr Donaldson said the Arrow River was last sample-tested in 2009, at which time it was not affected by didymo.
Sample testing ceased around that time because of how widespread the problem had become, with council staff carrying out observation tests instead.
''It's disappointing, but we haven't confirmed it yet.
''We always knew we were in trouble with the Arrow because we had it in the Matukituki and Motatapu.''
Mr Donaldson said while it was possible for didymo to be in an irrigation race and not a river, the likelihood was the Arrow was also affected, but it was unlikely to be noticeable.
''The thing about the Arrow River is it carries such a high sediment load, the sediment would act like a Steelo pad.
''The river itself is never going to develop a lot of material because of the sediment.''
The Queenstown Trails Trust, organiser of the Motatapu events, which include a 47km mountain bike race from Glendhu Bay through the Motatapu, Soho and Glencoe Stations finishing at Arrowtown, had a cleaning station at the summit to protect Arrowtown and the Wakatipu basin from lagarosiphon, a pest plant present in some of Otago's waterways, and didymo, Mr Donaldson said.
''The biggest mover of the organism is the human mover.
''We've tried to ensure that people going from an affected waterway to an unaffected waterway check, clean and dry.''
Signage was already in place around the Arrow River to educate users on didymo and how to prevent its spread.