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.