After the testing by the students, Kapiti Coast District Council erected temporary health warning signs but a definitive source of the pollution couldn't be pinpointed.
Rotting logs and other debris was removed from the stream but high levels of bacterial remained especially after heavy rain.
The university conducted an extensive two year water quality study of the stream and its tributaries to pinpoint the dominant faecal pollution sources of the stream.
From February 2013 to January 2015 the university collected and tested 317 water samples from 51 sites mainly along the Wainui and Te Puka streams.
Results in 2013 started off with 98 per cent of samples exceeding the 'action red mode' but later in the year only 23 per cent exceeded the action red mode.
It said "significantly" all the very high E.coli levels were found when livestock in two paddocks had access to unfenced areas of the streams.
Importantly, livestock were excluded from the farmland at the end of August 2013, and by October 2014, before the land was restocked, all the paddocks bordering both streams were fenced off.
During 2014, testing showed only 11 per cent exceeded the action red mode.
The report concluded the massive faecal pollution of the stream was caused by non-point pollution: primarily from agricultural run-off, when livestock had unrestricted access to unfenced streams in the farm land, storm water run-off sources, especially after heavy rainfall, and direct deposition of water fowl faeces.
Regardless of the improved water quality of the stream, the study doubted "whether the stream is, even now, entirely safe for recreational use" because the water quality would always fluctuate because of heavy rain discharging contaminated storm water run-off, low flows at some sites because of debris build-up, faecal pollution from livestock who gain access to unfenced or fenced areas, and duck faecal pollution.
Early last year the district council erected public health warning signs at nine sites along the stream.
