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Cow manure has been found to be the cause of ''alarming'' high levels of bacteria in the Taieri River near Waipiata this summer.
The site is part of the Otago Regional Council's annual summer water monitoring programme and six of the 17 samples taken between December and March exceeded Environment and Health ministries' ''action level'' for recreational water quality showing high levels of E. coli bacteria.
Council environmental information and science director John Threlfall said three of the high levels of bacteria at Waipiata were recorded in dry weather without a noticeable cause.
To be considered very safe for swimming, standards stated E. coli per 100ml should be below 260.
At Waipiata, on December 28, E. coli per 100ml was 1414 without rain. After rain on January 18, it reached 2420.
Only three of the 17 samples were under the first ''action level'' of more than 260 E. coli per 100ml.
The council sent water samples for faecal source tracking tests. The results showed the bacteria was from cows.
The high bacteria levels had not moved downstream to Outram because of dilution with more water.
''It's not a persistent problem all the way.''
The council investigated a complaint of stock in the river earlier this year but a helicopter fly-over did not find anything of concern, he said.
Environmental services manager Martin King said the compliance team would investigate.
This would involve council staff visiting the monitoring site and working their way upstream to see if they could detect ''anything untoward''.
It was the second mysterious freshwater pollution problem the council had encountered this summer.
Kakanui had three failed samples in dry weather and further investigation by the council found it was most likely due to a gull colony upstream from the gorge.
Overall, the council took 132 samples from December to March at freshwater sites and 84 at coastal sites to test for the concentration of bacteria such as E. coli.
Lake Hayes, Lake Waihola, the Taieri at Outram and the Waikouaiti at the wharf were suitable for swimming at all sampling times, Dr Threlfall said.
''Most sites were looking good, except for those few times after rainfall.''
Twenty-seven of 216 samples reached ''action level'' judged to be an unacceptable risk for swimming.
Some of the highest numbers were found in early January after heavy rainfall, which tended to wash faecal material into drains and then rivers.
The testing sites
Lake Hayes, Manuherikia at Galloway, Pomahaka at Glenkenich, Kaka Point, Lake Waihola, Otakia Creek at Brighton, Macandrew Bay, Taieri at Waipiata, Taieri at Outram, Waikouaiti at Bucklands, Waikouaiti at Wharf, Kakanui at Clifton and Kakanui Estuary.