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An Otago Regional Council investigation was launched last month, after E. coli tests taken at Clifton Falls revealed bacteria levels in the Kakanui River had breached the council's safety guidelines four times in December and January.
E.coli levels peaked at 2400 parts per 100ml of water on January 3, well above the council's aim to keep levels below 300 parts per 100ml.
Council resource science manager Matt Hickey said the levels had the potential to cause illness in swimmers, but staff were ''baffled'' when initial inspections of local farms failed to reveal any source of pollution.
However, an aerial survey, conducted by helicopter, finally revealed the source to be a large colony of nesting gulls.
Mr Hickey said the previously unknown colony was found in rugged terrain, 5km above the Clifton Falls Bridge.
He said a total of six colonies of gulls were found nesting on steep rocky faces.
While they had gone undetected until now, due to the inaccessibility of the gorge, it was likely the gulls returned each year to breed in the same places, he said.
''Unfortunately, these nesting gull colonies are likely to continue to cause high E.coli concentrations in the upper Kakanui River, particularly during the breeding season.
''Bird activity, river flow, or even whether it is a cloudy or sunny day, will influence actual bacteria numbers at Clifton Falls Bridge. With hindsight, it reflects the random nature of the historical bacteria results at this site.''
He added that water-quality samples taken upstream of the colony revealed E. coli concentrations of 214 parts per 100ml, whereas immediately downstream, the concentration was recorded at 1300 parts per 100ml.
Government water-quality guidelines for recreational swimming areas suggested that those with E. coli concentrations of less than 260 parts per 100ml should be safe, whereas water with more than 550 parts per 100ml could pose a health risk, he said.
Coastal Otago biodiversity programme manager David Agnew said the Department of Conservation would look into the situation and try to identify which species of gull were nesting in the area.
Mr Agnew said the species involved would determine what could be done to remove them.
''Black-backed gulls are not protected so that's not a problem as far as if they are causing a problem. They are not rare or threatened, they are not even protected, whereas red-billed gulls and black-billed gulls both have their own conservation concerns.''