The city council has applied to the Otago Regional Council to renew resource consents to discharge stormwater into the sea.
The city council is seeking 35-year consents to change its contaminant monitoring regime and merge the 10 existing consents into four, covering the discharge points of Andersons Bay, St Clair, Port Chalmers and the Otago Harbour basin.
The council says its new approach to managing stormwater aims to ensure no further degradation of those receiving environments.
Key priorities are resolving sewage stormwater cross-connections, reducing contaminant load in stormwater using source control where practical or otherwise effective treatment, and prioritising investment in that based on what the community is willing to pay and sacrifice as a result.
In their submissions, Save the Otago Peninsula (Stop), the Southern District Health Board (SDHB), the Department of Conservation (Doc), Port Otago and Te Runanga o Otakou called for more robust monitoring of the contaminants in stormwater.
Most suggested quantifying the level of existing contamination should be a condition of consent.
All said a 35-year term was too long - Doc and the SDHB said changes in stormwater treatment technology could be significant over 35 years, while Stop said any new monitoring regime should be reviewed at least every five years.
Doc was also concerned the council's proposed mixing zones were too large, and their strategy to monitor and reduce contamination was too complex.
It sought conditions that included careful monitoring of outfalls that serviced industrial or trade premises and investigation of the feasibility of removing significant contaminated sediment near outfalls.
It suggested the content of the discharge could be controlled by several methods including diverting stormwater from industrial or trade premises to the sewerage system or having it treated before discharge.
Port Otago was opposed because, it said, stormwater could contaminate spoil removed from the harbour in its dredging operation, limiting the options available for the spoil's disposal.
If the applications were not refused, it sought a condition that the council be responsible for the cost to Port Otago of removing any of the problem contaminants from spoil.
Clinton farmers Brent and David Mackie said the city council should be treated the same as the rural sector and the regional council should fine it for untreated wastewater going into waterways.
"The urban areas are just as environmentally unclean as the rural sector, why are they not being taken to the environmental court, fined and made to clean up their act, just like its rural cousins."
Brent Mackie said all water outfalls should be monitored and tested by an independent body.
David Mackie said there could not be two sets of rules, one for farmers and one for urban residents.
"How can the regional council take farmers to court for run-off from a paddock into a stream, when the city council can discharge into the sea at all times?"
The regional council has previously indicated new contaminant standards will eventually be set for stormwater discharge.
The city council has previously warned finding an affordable practical solution for improving water quality in urban stormwater systems would be a challenge.
It has applied for a panel of independent commissioners to hear the resource consent applications and a hearing date will be set after the panel is appointed.