Emergency services were called to Moto, on the NSW mid-north coast, on Wednesday afternoon and located the body of the 63-year-old.
NSW Police said he was in a house impacted by flooding and that a report will be prepared for the coroner.
Premier Chris Minns said communities in rain-affected areas along the north coast of the state need to brace for "more tough times" in the next two days.
"It's very sad, and when there's these terrible natural disasters, they hit ordinary families in terrible ways. and our heart goes out to obviously that man and his family," he told Nine's Today show on Thursday.
"I'm very grateful we've got thousands of volunteers and the local community has really rallied in the last 48 hours, but they've needed to."
The mid-north coast and Hunter regions have been the worst impacted by the flooding in recent days, with tens of thousands of people isolated and hundreds requiring rescuing.
The deluge has spread to the Northern Rivers and Northern Tablelands as a slow-moving trough dumped rain along Australia's east coast.
Falls between 200-300mm in the next 24 hours are likely and may lead to flash flooding, the Bureau of Meteorology warns, around the north coast communities of Coffs Harbour, Port Macquarie, Taree, Woolgoolga, Sawtell and Dorrigo.
The bureau said the trough was expected to contract southwards on Thursday afternoon.
More than 100 warnings are in place, with local residents in the path of flooding urged to head to higher ground and evacuate if they can.
SES Assistant Commissioner Colin Malone said conditions through the night into Thursday had been challenging.
"We've seen continual rainfall and very fast flowing rivers which, when combined with flooded roads, have made it very difficult to access some isolated people," he said.
"While dozens of rescues have been completed overnight, they continue to be received."
In the past 24 hours, the SES has carried out about 340 flood rescues and used helicopters to winch stranded residents off their roofs as they responded to 1023 incidents.
More than 100 rescues were outstanding on Thursday morning, the SES said.
Some 50,000 people have been warned they could be isolated on Thursday. including in Kempsey on the mid-north coast where the Macleay River has overtopped a levee and is still rising.
Major flooding will continue to impact other nearby areas like Macksville and Port Macquarie.
Farmers have lost livestock washed away by floodwaters.
Others are working to help get some of them back, taking to community Facebook pages to track down owners for cattle that have washed up on their properties.
Evacuation centres have been set up at Dungog, Gloucester, Taree, Manning Point, Wingham, Bulahdelah, Tuncurry Beach, Kempsey and Port Macquarie.
Emergency Management Minister Kristy McBain said the Commonwealth was working with the NSW government to provide support in 16 local government areas.
The Insurance Council of Australia said the flooding could be catastrophic, with significant flooding in similar areas in 2022.
"We are closely monitoring the severe weather across the entire state," council chief executive Andrew Hall said.
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