Floodwaters could breach a rail line and flood a township on the northern outskirts of Adelaide, authorities warn.
The State Emergency Service issued an emergency warning for Virginia on Saturday night, with residents alerted by text message about 6.30pm to enact their flood plans.
The Gawler River had already broken its banks at Virginia by Saturday morning.
"Floodwater is flowing along the eastern side of the railway line and there is a risk the water will breach the railway line and flood the Virginia township," an SES spokeswoman said.
Emergency warnings for other areas in the Gawler catchment, including Gawler, Hillier, Gawler River, Angle Vale, Penfield Gardens, Two Wells, Lewiston, Port Gawler and Buckland Park, also remain in place.
Earlier, a flood warning for Port Wakefield was downgraded from an emergency to a watch and act due to floodwaters stabilising.
Residents were, however, warned a small increase in water levels was expected during the night.
Road closures and diversions also remain in place.
"Although floodwaters are no longer rising, significant amounts of water are still present which may threaten the safety of you and your family," the alert warns.
An extra 60,000 sandbags were flown into SA to protect property and additional personnel support is being provided by WA, Victoria and the Australian Defence Force.
Earlier on Saturday, Premier Jay Weatherilll said about 20 structures around the town of Balaclava had been impacted, but authorities weren't sure if they were houses.
Homes had been flooded at Old Noarlunga as well.
The extent of the damage will not be known until the waters subside.
The deep low pressure system which caused the havoc has moved away from Adelaide and while flooding is stabilising around the Angas and Bremer catchments, the SES is advising people to remain vigilant.
The SES is also reminding residents not to walk, ride or drive through floodwater, or allow children to play in or near floodwater.
