Burundi informal settlement residents, near Mfuleni, had called to be evacuated from the area.
The SA Weather Service said rain would continue over Cape Town, the Cape Winelands, and the western parts of the Overberg until Thursday evening.
Acting mayco member for human settlements Grant Twigg said measures were in place to mitigate inevitable winter storms and flooding in high-risk areas, with at least 29 informal settlements identified as high risk.
The majority of the high-risk areas are situated along the N2 and in Khayelitsha.
Burundi community leader Nathi Mgxokwana said residents had complained of not being evacuated since 2015, when they were promised people would be taken to a newly built area in Mfuleni when it stormed.
“The last time people were evacuated was in 2009. The conditions are unbearable during and after the heavy rains.
“Officials must come and see for themselves.
“The smell from the water pipes is too much, as they haven’t been cleaned since the beginning of the year. This is hazardous for our children who most of the time play outside and it’s unsafe for them to be exposed in such an environment,” Mgxokwana said.
Disatser management spokesperson Charlotte Powell said in flooded areas the ground had been assessed, and dwellings were found to need plastic sheeting.
“In Imizamo Yethu, a tree was uprooted and fell on two informal dwellings.
“The recreation and parks department has been requested to remove the tree. The roads, infrastructure and management department is still busy clearing stormwater systems in the affected areas of Gugulethu and Mitchells Plain.
“The disaster operations centre is still receiving calls from the public due to Wednesday night’s flooding and these assessments will be done during the course of the day,” added Powell.
Other areas affected included Gatesville, Diep River, Athlone and Wallace Dene.
In Manenberg, the canal in Silverstream Road had overflowed, leaving a number of houses flooded.
Officials attributed the cause of most flooded areas to blocked drains, mostly as a result of illegal dumping in to the city’s storm water system.