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Some Dunedin residents are flushing their toilets straight into the sea without even being aware of it.
The problem of sewerage pipes being accidentally or deliberately connected to stormwater pipes has resurfaced.
The council has been delving deeply into its stormwater management as it prepares to renew resource consents, due to expire in November.
In a report, water and waste services manager Laura McElhone said "cross connections" between stormwater and sewage pipes were thought to have been mostly fixed over the past 25 years.
Intensive testing over the past four years shows half of the city's 10 stormwater catchments have some faecal contamination, likely to be coming from sewage pipes.
"Once located these will be resolved as a priority."
It was very difficult to find the exact locations of sewage contamination. Harbour water quality was "generally suitable for contact recreation" but that might not be the case near stormwater outfalls, she said.
Infrastructure services committee chairman Andrew Noone said the council was worried the Otago Regional Council would require stormwater to be treated.
The cheapest treatment option was $2 million and the most expensive was $87 million.
The council has already budgeted $2.6 million over three years to improve stormwater quality, including $1.5 million to prevent sewer pipes overflowing into the wastewater system at Murray St.
Cr Noone said stormwater quality was a "significant community concern" and the DCC's Three Waters strategy was developed to improve it.
A bylaw was being considered that would bring all of the existing rules together and require more preventive measures by developers of subdivisions.
Cr Noone said the DCC would prefer the concept of "reasonable mixing" where some contaminated water could be released into the sea as long as it posed no risk to the wider ecosystem, public health or recreation values.
ORC chairman Stephen Woodhead announced at the end of April this year that the ORC was changing the rules to improve discharges from urban stormwater systems.
He said there were many treatment options available to councils and waterways had to be protected from "degradation by stormwater discharges".