Evacuation centres have been established either side of the river for displaced residents.
Moderate flooding was occurring at Windsor overnight while Penrith on Sydney’s western fringe had minor flooding.
Meanwhile, coastal erosion was expected along the south coast as strong to gale-force winds drove large waves on to the coast overnight.
More than 100mm fell in Nimmitabel in the Bega Valley on Saturday as the weather system began to move south into the Tasman Sea.
More than 107 warnings were in place late on Saturday night. The rain on Friday and Saturday earlier caused landslips, flash flooding and a house in Wollongong to be swept into a creek.
Witnesses reported seeing two people emerge from the mangled home in Mount Keira.
Investigations on Sunday will also continue into the death of a man found in water in Penrith.
The man, whose death was not attributed to a cause, was located by a passer-by about 7.30am on Saturday.
SES crews rescued scores of people from their vehicles with almost half of the 168 flood rescues statewide in metro areas.
Lakes and lagoons overflowed into roads and residences while numerous national parks were closed including urban oasis Lane Cove National Park.
Trains across the Sydney and NSW rail networks faced significant delays and gaps in service into Saturday night due to flooding affecting infrastructure in various locations.
Commuters were advised to avoid travel or allow plenty of extra time.
An overflowing Parramatta Weir was also continuing to stop river ferry services from going further upstream of Rydalmere.
Almost a dozen evacuation alerts were in place overnight but conditions elsewhere were expected to ease.
Partly cloudy conditions were forecast for the hardest-hit areas including Sydney and Wollongong.
Scattered showers were expected about the southern and central slopes and ranges, and the NSW southeast.
- AAP