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The Otago Regional Council yesterday confirmed the Arrow River has tested positive for didymo.
In March the Otago Daily Times reported a sample taken from the irrigation scheme at The Hills had tested positive, prompting the ORC to test the Arrow River, which had previously been clear.
Although surrounding rivers, including the Motatapu, Shotover and Kawarau, were infected with the micro-organism, also known as rock snot, it had been hoped the spread into the Arrow could be stopped.
However, ORC environmental monitoring director Jeff Donaldson said yesterday attempts to prevent the organism's spread into the Arrow were unsuccessful.
''It's disappointing but it probably wasn't unexpected. There's a lot of recreational activity in that area, particularly over summer months.
''It was a river that was probably a little bit harder to identify it in ...
''People won't recognise it in your waterways ... you have that high sediment movement ... you will never find biomass building up.''
Signs were already in place around the river to educate users on didymo and how to prevent its spread and Mr Donaldson said they would stay.
''We don't put up signs to say 'This waterway is affected' ... We want people to change their behaviours on every waterway.''
Despite a large number of rivers and lakes in the wider Otago area being affected, the focus remained on those which were still ''pristine'', including the Taieri River and lakes including the Poolburn, Manorburn and the Blue Lake.