Charlotte Powell, a spokeswoman for Cape Town’s disaster and emergency management, said around 9000 people from 2500 shacks had been affected by the floods.
No injuries had been reported.
"We are mopping up across city," she said. "We have 20 informal settlements that have been affected. They are mostly on the Cape Flats."
Emergency sheltering was being provided for the affected people in community halls. Powell said the Lourens River in Strand and Liesbeek River outside the city had burst their banks.
She said floods had also hit suburbs such as Newlands, Rondebosch, Claremont, Athlone and Somerset West.