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The Radius Fulton Care Centre in Hillside Rd was evacuated earlier this month after wastewater flowed through the building, damaging the carpets and skirting boards.
Some residents were relocated as far away as Invercargill.
Facility manager Robyn Bowie said the wastewater came back through the building's shower drain pipes.
Unlike in 2015, when flooding severely damaged two wings of the building, the damage this time was less severe and the repairs were not as extensive, Mrs Bowie said.
She was unable to say how much the repairs would cost.
Some residents would move back in on Monday but it would be at least another month before they were all able to return, she said.
Because of repeated flooding issues, the owner of the building, Radius Properties, had been investigating ways to lessen the damage, such as back-flow prevention valves.
But because much of the problem was due to South Dunedin's wastewater infrastructure, there was only so much the company could do.
''You can imagine, 93 residents live here and all their homes were destroyed and it's going to take at least another three to four years for the council to do something.''
''I just find it staggering.''
The evacuation had been traumatic and difficult for both the residents and their families, she said.
A Dunedin City Council spokeswoman said council staff visited the care home during the flooding and short- and long-term options to mitigate flooding in South Dunedin were being worked on.
In its draft 10-year plan, the council has proposed spending $43 million on stormwater improvements in South Dunedin and on an upgrade of the Green Island wastewater treatment plant.
Both aim to reduce wastewater flooding in South Dunedin.
Because of the size of the projects, it was likely the focus in the next two to three years would be on planning and design, the spokeswoman said.