The 68-year-old man was found in a submerged van at Cobbity before 8am on Friday.
His body was retrieved about 1pm following an operation by police divers and the SES but he is yet to be formally identified.
More than 150 NSW schools have been closed after heavy rain and flooding prompted evacuations in Sydney's south and southwest.
Evacuation orders are current in 11 suburbs, while residents in a number of other areas have been told to prepare for orders to leave, many of them in locations evacuated during flooding in March.
The Hawkesbury-Nepean Valley is being monitored, with major flooding expected on Friday.
Residents in Chipping Norton, Woronora and Bonnet Bay in Sydney's southwest have been given the all clear to return home after being ordered to evacuate on Thursday.
NSW Premier Dominic Perrottet said close to 2400 people were subject to evacuation orders on Friday morning, with more than 17,000 in the warning areas.
"Despite the substantial flooding that we've seen across our state, what is incredibly pleasing has been that we've only lost a very few amount of lives, and that has occurred because of the efforts that everyone has made across our state in following the instructions of the SES," Mr Perrottet said, before the news that the man's body had been discovered.
Emergency Services Minister Steph Cooke said the state had flood fatigue but people needed to keep following the advice of emergency services.
"It will stop raining, it will get better," Ms Cooke said.
"We just need to keep (getting) through this one day at a time."
The Bureau of Meteorology's Jane Golding said the rain would ease on Friday after downpours on Thursday.
"We do have flood warnings current, though, so although the rain is easing ... the rivers will be moving quickly (and) there's a lot of debris flowing around," she said.
The SES received almost 1200 requests for assistance and conducted 35 rescues in the 24 hours to 9am on Friday.
"Across a population base the size that we had under warning areas, 35 is actually quite a low number and we are really grateful for the community for listening," NSW SES acting commissioner Daniel Austin said.
More than 1200 SES volunteers have been on the ground.
The NSW education department has listed 155 public schools, predominantly around Greater Sydney, the Illawarra and Shoalhaven regions that are not operating due to adverse weather conditions as of Friday morning.
Central and South Coast rivers are no longer subject to flood watch, but danger remains in the Hawkesbury-Nepean.
Water is spilling over Warragamba Dam, which was at capacity when the downpour started.
A major flood peak above levels seen during the April 1988 floods passed through Menangle on Thursday afternoon.
Wallacia is expected to experience flooding at levels higher than last month when the Upper Nepean River peaks on Friday.
There is also major flooding likely on Friday afternoon at North Richmond on the Hawkesbury River, although the Bureau of Meteorology believes it will remain well below last month's flooding.
21°C