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An aerial survey of the upper Taieri River will be completed this week, as the Otago Regional Council tries to pinpoint the source of the water's high bacteria levels.
Signs warning of E. coli were placed at popular swimming holes in the area several weeks ago, and the council has been trying to find out why the bacteria continues to be a problem.
ORC director environmental monitoring and operations Jeff Donaldson said staff had been tracking the river and its tributaries through properties in the area.
They had also kayaked the river but were unable to identify a definite source.
While this week's aerial survey was conducted, staff would track the effects of irrigation operating in the area, Mr Donaldson said.
''We will also extend our weekly recreational sampling programme on the upper Taieri by another two months from the usual conclusion on March 31, to help us understand what is happening in this catchment to cause this problem.''
Many factors could affect bacteria levels in waterways, he said.
Extensive property inspections had shown upper Taieri farmers generally adopted good water quality practices, including keeping stock out of waterways, he said.
''Upper Taieri E. coli levels monitored as part of our weekly recreational sampling programme have fluctuated over the summer, and samples have not all been at alert levels, which has also made it difficult to pinpoint a single source.''
Recent tests showed high bacteria levels, which would be presented by the council at a public meeting in Patearoa, Mr Donaldson said.