Otago Regional Council resource management director Selva Selvarajah said the council was notifying the application because it would have more than minor effects on the environment and special circumstances applied because all affected parties could not be easily identified.
The discharges occur at 31 outfall locations within Otago Harbour, as well as from two outfalls at St Clair Beach and a single outfall at Second Beach.
The notification notice says the stormwater discharges may contain contaminants attributed to runoff from the various land-use activities within the Dunedin and Port Chalmers areas.
"The stormwater is untreated before entering the coastal environment and may not meet contact recreation water quality standards."
People would have 20 working days to make a submission. A hearing would be held within 25 working days after that, Dr Selvarajah said.