People have been advised not to go swimming in Dunedin beaches. Photo: Getty Images/File

Dunedin residents are being urged to stay out of the water at popular beaches and Otago Harbour for the next two days, after partially-treated wastewater was discharged into the sea.

Dunedin Civil Defence controller Sandy Graham said heavy rain had caused the partially-treated wastewater to be discharged.

Swimmers, surfers and shellfish gatherers were urged to avoid the water around Lawyer’s Head, St Clair, St Kilda, Tomahawk and Smails beaches, as well as Otago Harbour, she said.

The heavy rain had caused ‘‘a significant combination of stormwater and wastewater’’ to enter the Tahuna wastewater treatment plant.

In order to limit the chance of flooding in South Dunedin, the Lawyers Head outfall was opened last night.

“Obviously, there are health risks associated with partially treated wastewater so we need people to stay clear of the water for 48 hours,’’ she said.

Council contractors were checking roads, stormwater and wastewater infrastructure and removing debris.

Some roads remained closed and were likely to be closed for most of today.

For Dunedin City road conditions and other weather-related information, visit www.dunedin.govt.nz/news-and-events/public-notices/alerts/weather-inform.... For any urgent issues, please call 03 477 4000.

Nine people chose to take up the offer of emergency accommodation at Aquinas College.

Ms Graham said: "Now that the city is returning to normal, we’re able to support our Clutha neighbours who are under a State of Emergency and are experiencing far worse conditions, by providing staff and resources to help them through this difficult time."