Bacteria levels in the Taieri River at Waipiata, a popular bathing spot, continue to be up to three times higher than the national health guidelines, making it unsafe for swimming.
Bacteria levels have exceeded the red action guideline of more than 550 E. coli per 100ml - which indicates the water posed an unacceptable health risk to swimmers - in every Otago Regional Council test this summer has shown.
On December 23, it recorded 1986 E.coli per 100ml after significant rainfall two days earlier, but on December 30 it recorded 770 E.coli per 100ml without rainfall in the previous days.
Last year, the council launched an investigation after unexplained levels of bacteria were recorded three times during last summer's recreational monitoring programme.
The regional council monitors the water quality at popular marine and freshwater bathing sites once a week between December and March.
It tested for the concentration of bacteria, Escherichia coli in freshwater or Enterococci in salty water, which indicated the presence of faecal material and disease-causing organisms.
Council environmental services manager Martin King said yesterday two staff last summer investigated the small tributaries which entered the river nearby, seeking sources for the contamination but no obvious source was found.
"It seems it could be a mix of a number of things."
Many water fowl had been seen in the back waters and there was the potential for irrigation run-off.
"There's a raft of things really, but we came to no major conclusions."
Staff would meet in coming weeks to analyse the recent Waipiata data to see what else could be done, he said.
"There is a bit of work to be done, but to be honest there is no quick and easy fix."