He said council officers thought the water was stormwater but they were still unclear about its origin.
"We did an inspection of the stream for any obvious signs of a wastewater spill, but could not see any of the usual signs.
"We will follow up with the private property owner to find out what is causing the constant flow of water through the stormwater outlet into the stream," Mr Benadie said.
He said it appeared that the water spilling into the stream was not wastewater from the overflow of the Tangi St pump station.
Tangi St pump station was equipped with new electronics that record any problems at the station and and none had been found.
Mowhanau Stream, a popular spot for swimming and paddling, has had ongoing problems with bacteria levels over the years.
In December 2010, Horizons Regional Council's water spokesman, Barry Gilliland, warned that bacteria levels in the stream were "above trigger level", although not as high as they had been.
"There have never been health problems reported from people swimming there, but they are still urged not to put their heads under or swallow water," Mr Gilliland said.