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Clutha Valley sheep and beef farmer Evan Williams told the Otago Daily Times he was ''surprised'' to find little public attention paid to the issue.
He said Environment Southland had published reports on its water catchments in May, which identified avian E. coli as a key source of bacterial waterway pollution, particularly in normal flow conditions, when people were most likely to be swimming.
The report ''Sources of Pollution in the Mataura Freshwater Management Unit'', prepared by crown research institute ESR for Southland, states ''direct deposition by birds is considered to be an important source of faecal contamination under base flow conditions''.
That meant regional councils - including Otago - should be looking more widely to improve water quality under the reforms, Mr Williams said.
''At the moment farmers are being blamed wholly for the problem. Clearly farming isn't entirely blameless and can play its part in reforms, but I'm not alone in wanting to see those reforms based on a fair assessment of the science.
''If the science is saying there are other sources of contaminants contributing to the problem, why aren't we hearing about that?''
Otago Regional Council (ORC) environmental resource scientist Rachel Ozanne said the council only conducted discriminatory testing of E. coli sources from lakes Wanaka, Wakatipu, and Hayes.
This had identified birdlife as responsible for spikes in E. coli at Queenstown Bay in January.
Field surveys had also identified nesting black-billed gulls as responsible for elevated E.coli levels in the Upper Kakanui last year.
Other monitoring sites on the region's rivers were not subjected to ''faecal source tracking'' at present, she said.
Tapanui farm consultant Lloyd McCall, who helped establish the award-winning pathway for the Pomahaka farmer-led catchment water quality improvement group, said the cost of source tracking could be an obstacle.
''Unfortunately it's about $1000 a test at present. It's certainly something we've considered, and something we've talked about with ORC.''
As part of its work, the group was collating data on total E. coli levels above and below duck ponds, which it would discuss with the council when complete.
''At that point we can say in an informed way, 'Ducks may be an issue'. So it's definitely on the radar.''
Federated Farmers environment and water spokesman Chris Allen also acknowledged the current lack of detailed information as an issue.
''Information is king in this area. In my home patch on the Ashburton River, a debate raged for about 30 years as to whether farmers or birds were responsible for summer spikes in E.coli testing.
''Recently, [faecal source tracking] identified birds as the issue. This is not to say farming has no effect, but we've got to acknowledge all sources and their relative effects in order to address the underlying causes effectively.
''The techniques are out there to help us get to the bottom of things. Let's use them.''