With no major rain forecast for at least a week, the huge task of cleaning up can begin.
New South Wales Health is warning residents to be aware of the risk of contamination and the water-borne diseases during the clean up.
"Many parts of NSW have been badly affected by flooding and some people are beginning to return home," Dr Adi Vyas, acting director of environmental health at NSW Health, said.
"Though this will be a distressing and difficult experience, we want to remind people of the need to be safe when cleaning up their home to protect their health.
"Floodwater can be extremely polluted and contaminated with sewage and chemicals. Contact can lead to skin and stomach infections and other rare, but serious conditions, such as leptospirosis."
More than a dozen evacuation orders remain, and about 60,000 people are on standby to evacuate, with major flood warnings still in place for the Macintyre, Gwydir, Clarence, Hawkesbury, Nepean and Colo rivers.
Some of the 20,000 people forced to leave in NSW have been cleared to return home.
The SES issued an all-clear notice for parts of Greystanes in Sydney's west, and the Kempsey CBD and nearby areas.
Hydrologist Victoria Dodds said flood warnings would likely remain in force across the state, particularly in inland areas, for the days and weeks ahead.
Premier Gladys Berejiklian pleaded with people to stay out of floodwaters after two drivers died trapped in their cars.
A man died in Glenorie in northwest Sydney on Wednesday and the body of another man was found submerged in a ute in Queensland's southeast.
"You may have heard your local river has peaked or that the worst of the rising waters may have may have ceased (but) the currents underneath the surface are very strong and the flows are doing things that they don't normally do," she said.
There have been 11,000 calls for help to the NSW State Emergency Service, and 950 flood rescues.
Fire and Rescue NSW have also rescued three people who were swallowed by a sinkhole near the Mehi River in Moree, where major flooding is occurring.
There is still significant flooding along a number of rivers, but the focus has turned to the northern rivers region, particularly Grafton, Maclean and Ulmarra.
Those in low-lying areas of Ulmarra, Bushgrove and Cowper were ordered to leave on Wednesday afternoon.
Major flooding is also occurring along the Hawkesbury River and authorities say it's likely to continue in North Richmond and Windsor until the end of the week.
Moree in the northwest, the Upper Hunter around Singleton and parts of the Central Coast are still of concern.
Eighty-nine schools remain closed across the state.
Federal Energy Minister Angus Taylor said while tens of thousands of customers have had their electricity restored, about 3600 customers were still without power.
Access to flood areas remains difficult, with some cables still submerged.
Defence and emergency service personnel are flying in essential supplies to isolated communities, particularly North Richmond.
ADF members have already been embedded in emergency operations centres in areas of concern, and are part of teams assisting with damage assessments.
The defence force's role will be stepped up to a force of about 700, with troops brought in from northern NSW and Newcastle.
"As soon as the all clear has been given, we'll assist with those SES-lead teams in assisting with the clean up," ADF Brigadier Mick Garraway said.
Resilience NSW Commissioner Shane Fitzsimmons said the clean-up would be dirty, emotional work for the communities, many of which were hit by drought and bushfire before the floods.
"When you think about the last 18 months to two years ... our hearts break for these people," he told Nine's Today Show.
