Too much bird poo in a popular Bay of Plenty swimming spot has prompted an investigation following a warning from health authorities.

Bay of Plenty Regional Council has confirmed it has found high levels of E.coli in the Uretara River, near Katikati, in recent river monitoring work.

The regional council was now looking into what was causing the high levels of bacteria after Toi Te Ora Public Health issued a health warning advising the public to avoid swimming in the river in December.

To find the source of the bacteria the regional council set up 13 additional monitoring sites upstream of the popular Henry Road Ford swimming hole, to test both the water and sediments.

Regional council land management officer Braden Rowson said the testing identified the bacteria was predominantly from birds, with one key site showing extremely high levels of avian faecal matter in the sediments.

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"This upstream site had become home to a number of birds including a flock of nesting geese with hatchlings and a high number of resident pūkeko. They poo in and around the water which then flows downstream affecting the waterway," Rowson said.

The landowner had since removed the geese from the site however it would still be a while until E.coli levels started to fall.

"The E.Coli remains in the sediments and as it is disturbed it will continue to affect water quality. But without being stirred up it will not get flushed out of the river system," Rowson said.

Bird poo may not be the only contributing factor and the regional council would also meet with landowners to see whether any activity on their land may be contributing to the increased bacteria levels and if so would explore ways to prevent it.

"Working with the community we want to better understand the impact natural fertilisers like chicken manure may be having and how we can better manage that impact," Rowson said.

Toi Te Ora Public Health advised people to avoid swimming in the river and parents should particularly make sure their children did not paddle or play in the river.

To check if an area is safe to swim, visit www.lawa.co.nz.