But an Otago regional councillor called out the council itself for putting the blame on irrigators at one of them.
A report to the Otago Regional Council’s environmental science and policy committee said last summer 560 routine samples for faecal indicator bacteria were taken at 33 sites, and 93% of samples had water quality that was "suitable for swimming" at the time of sampling.
The staff report singled out Waianakarua River at Graves Dam, Kakanui Estuary and Manuherikia River at Shaky Bridge as waterways with issues.
Those sites had "markedly more exceedances" than others.
At all three sites, 40% or more of the tests done over the season showed elevated E. coli levels, the report said.
It said gull colonies upstream were responsible for the high E. coli concentrations at Waianakarua River.
Low flows — and as a result an extended period of time with the estuary mouth closed — produced repeatedly raised bacteria concentrations at Kakanui Estuary.
Faecal-source tracking at the Manuherikia River site indicated ruminant, and avian, sources for the high levels of bacteria recorded there.
"While high bacteria levels were observed following rainfall, they were also persistent throughout the low-flow period," the report said.
"It is likely that irrigation by-wash is a key source of bacterial contamination during low-flow periods."
At last week’s meeting, Cr Gary Kelliher questioned why irrigation by-wash had been honed in on and what basis the council had for implicating irrigation companies.
Cr Kelliher said the Manuherikia catchment had experienced its "worst season in 40 years".
"It was drawn down to a lower level than empty, because there is such a thing as lower than empty with Falls Dam," Cr Kelliher said.
"There was a lot of concern across the community.
"By putting ‘by-wash’ there you immediately implicate the directors of the irrigation companies."
He asked whether any testing had been done to back up the claim.
Council science manager Tom Dyer conceded staff were generalising and "probably" mixing up by-wash with runoff.
Mr Dyer said "irrigation-related activities" might have been a better term to use.
"This is a generalisation and it’s a discussion point but it’s also reasonably likely to be accurate," he said.
"The intention was not to point fingers at anyone in particular.
"It was rather to acknowledge that there was a set of activities occurring in a place that likely — more than likely — had a link to some of the results that are presented in this report."
Chief executive Richard Saunders said staff’s job was to consider what the cause of the issues identified in the report might be.
"I take the point that if we are going to draw any form of conclusion we need to be careful with the language that we use.
"And if they are conclusions based on ‘our assessment’ . . . rather than based on ‘testing’, then we need to be clear on that.
"So, we can go away and have a think about the language that we use in these reports in the future and the consideration that we give to all the factors that might influence these results."
