People have been warned not to swim in the area, after water samples taken from the Taieri River between Creamery Rd and Waipiata on January 13, showed E. coli levels at 1500/100ml.
Government water quality guidelines for recreational swimming areas stipulate those with less than 260 E. coli/100ml should be safe, whereas water with more than 550 E. coli/100ml poses a health risk.
As a result, the ORC is erecting warning signs at popular swimming holes in the area.
The Public Health South medical officer of health, Marion Poore, said that high levels of E. coli had the potential to cause illness if swimmers swallowed the contaminated water.
''We strongly recommend avoiding these areas, and if you are feeling sick, with vomiting and/or diarrhoea from having swum in or swallowed contaminated water, contact your GP,'' Dr Poore said.
ORC engineering, hazards and science director Gavin Palmer said bird activity, river flow and stock in waterways could influence bacterial counts, but said a cloudy day could also influence counts, because E. coli often died quickly in clear water when exposed to sunlight.
''Local farmers have been notified of the problem and asked to keep a watch on stock near waterways, ensuring they do not have access to the river,'' Dr Palmer said.
ORC staff had conducted extensive ground inspections, tracking the river through adjacent farms, but have not found any conclusive cause of the E. coli contamination, he said.
Inspections of the river and tributaries by kayak have also failed to find any clear cause.
In every ORC test conducted this summer, bacteria levels have exceeded the red action guideline of more than 550 E. coli per 100ml.
On December 23, 1986 E. coli per 100ml was recorded after significant rainfall two days earlier, but on December 30 it recorded 770 E. coli per 100ml without any rainfall in previous the days.
Further inspections and water quality testing of the river are planned this week, he said.
Those wanting to find out when the water is safe to swim in again, have been advised to visit www.orc.govt.nz or contact the ORC.