More rain was expected in parts of the Western Cape on Saturday, the SA Weather Service said.
"Areas at risk, which will be affected the most, were the South coastal areas, George, Riversdale, Hermanus and Oudtshoorn," forecaster Ransby Bulo said.
He said the rain would continue into Sunday.
Provincial disaster management spokeswoman Charlotte Powell said systems were in place to ensure people were protected from floods.
"An area survey will be carried out to determine the [current] extent of flooding," she said.
Powell said a disaster response team was conducting a continuous assessment and taking extra measures to restore electricity and ensure draining water systems were functional.
Persistent rain had caused the Lourensford River to burst its banks.
She said 70 residents from Kays Caravan Park were placed at the Garden Village hall and 129 patients were evacuated at the Vergelegen Mediclinic in Somerset West on Friday night and taken to neighbouring hospitals.
Earlier, the National Sea Rescue Institute (NSRI) said members brought sea rescue vehicles and jet-ski's to rescue the patients.
Photos on social media site Twitter showed nurses pushing stretchers down a hospital corridor through water knee-deep.
NSRI spokesman Craig Lambinon said that by 2.30am on Saturday, most patients and staff had been evacuated.
Provincial department of transport spokesman Al-Ameen Kafaar said Chapman's Peak drive in Cape Town was closed until further notice.
"A maintenance team is busy clearing up the debris on the road." – Sapa