People have been warned to avoid contact with water in the Normanville Creek and Bungala River,
This comes after a system fault at SA Water's nearby Normanville Wastewater Treatment Plant which saw untreated wastewater discharged into the creek that joins the river and then discharges into the sea.
The Department for Health and Wellbeing's Principal Water Quality Adviser Dr David Cunliffe said one megalitre of wastewater had been released.
"We're also asking people to avoid contact with the seawater, 100 metres each side of the river outlet at Normanville Beach," Dr Cunliffe said.
"The affected areas are being clearly marked with signage, and the Environment Protection Authority (EPA) has attended the site to assess. People who come into contact with un-treated wastewater could experience gastrointestinal illness, including diarrhoea and vomiting.
"Anyone who suspects they have been in contact with wastewater in this area and are experiencing symptoms should speak to their GP or healthcare provider."
The fault at the wastewater treatment plant was identified by SA Water staff completing routine checks, who immediately notified SA Health and the EPA.
SA Water's Senior Manager Production and Treatment Lisa Hannant, said a thorough investigation would be undertaken into the incident.
"Our top priority will be understanding what happened, to make sure it doesn't happen again," Ms Hannant said. "The plant has returned to normal operation and additional monitoring is in place.
"We apologise for the inconvenience this incident may cause river, creek and beach visitors and assure the community that steps will be taken to prevent a recurrence.
"We will work with the EPA to assess localised clean-up options and any necessary actions to monitor and rehabilitate the affected watercourses. Water samples have been collected from several downstream locations from the treatment plant to determine the extent of the discharge, with results expected within the next 24 hours."
District Council of Yankalilla Mayor Glen Rowlands said, "SA Health have advised our Environmental Health Officer that an event like this generally runs for five days and that water samples will be tested until the levels return to normal and then the precautionary exclusion zone signage will be removed".
"The precautionary exclusion zone only includes 100 meters of Normanville Beach either side of the Bungala River outlet.
"This area is generally used for boat launching and not the main swimming area at Normanville Beach.
"While it's only a short stroll to find a safe place to swim at Normanville Beach our district boasts 90 kilometres of coastline including stunning rugged cliffs and 30 kms of spectacular white sandy beaches so you don't have to go far to find an alternate beach if you wish.
"The Jetty Caravan Park Normanville are not experiencing any effects to their services and have confirmed no visual changes or odours are currently present.
"They are looking forward to welcoming visitors for the October School holiday's and only have a few vacancies left, so get in quick.
"Protecting and caring for our pristine environment is a priority for Council our Community".
Shadow Minister for Water Susan Close said Water Minister David Speirs must explain what went wrong with the waste water treatment plant in Normanville.
"At a time when South Australians are being asked to holiday in their own backyards, one of our premier tourist beaches has had a million litres of waste leaked into the local waterways," Ms Close said.
"Minister Speirs must ensure this mess is cleaned up in time for school holidays and that it does not happen again."
SA Water will work with the EPA to assess localised clean-up options and any necessary actions to monitor and rehabilitate the affected watercourses.