The sole sailor, aged in his 70s, fell overboard from his vessel near the mouth of Breakfast Creek around 4.45pm on Saturday.
Three water police vessels searched for him until nightfall but their efforts were suspended due to dangerous weather and debris in the river.
The search resumed at first light Sunday, involving water police vessels, general duties officers, coastguard personnel and volunteers.
Meanwhile, severe weather warnings are in place from Bundaberg in the Wide Bay-Burnett region of Queensland through to Port Macquarie on the NSW mid north coast.
A "completely unpredictable" extreme rain event has killed six people in the northern state, with hundreds evacuated.
Overnight on Sunday, a man died in the Brisbane suburb of Indooroopilly when his car became submerged. The 34-year-old tried to swim to safety but witnesses raised the alarm when he failed to surface.
On Saturday, police divers found the body of a 37-year-old man in floodwaters near Gympie, north of the Sunshine Coast, while that of a 54-year-old man was discovered at Stones Corner in inner Brisbane.
A female SES volunteer was also killed when a car she was in was swept away en route to a rescue near Ipswich on Friday night.
The deaths follow those of a 54-year-old man killed trying to ride a motorbike through rising water at Gympie last week and a 63-year-old found dead in a submerged car on the Sunshine Coast.
In NSW, a man died on the Central Coast on Friday morning after his LandCruiser was carried away by floodwaters.
Queensland's Deputy Police Commissioner Steve Gollschewski has urged people not to leave home unless absolutely necessary.
In Gympie, 700 people along the swollen Mary River - expected to rise above its highest level in 23 years in the next 24 hours - began evacuating, while supplies were delivered to an Indigenous community in nearby Cherbourg set to be cut off by floodwaters.
Heavy rain and potential flash flooding are forecast from Kingaroy through to the NSW border on Sunday and intense falls are predicted for an area encompassing Hervey Bay, Yarraman, Toowoomba and Ipswich.
There is major flooding at Tewantin near Noosa and Picnic Point and Dunethin Rock on the Sunshine Coast, while flood warnings are in place for multiple waterways.
Brisbane Lord Mayor Adrian Schrinner on Saturday evening issued a warning for 16 suburbs along the Brisbane River, saying "several thousand properties" could be inundated.
Water is being released from Brisbane's Wivenhoe Dam. The Moogerah Dam, inland from the Gold Coast, is also spilling, as is the Atkinson Dam.
In NSW, a severe weather alert for Sunday spans 450km from the Queensland border to Port Macquarie.
There is a risk of "life-threatening flash flooding particularly during Sunday afternoon and evening" across the Northern Rivers and Mid North Coast, in areas including Lismore, Grafton, Coffs Harbour and Dorrigo, said Gabrielle Woodhouse, Senior Meteorologist from the Bureau of Meteorology.
On Sunday and into Monday, the Northern Rivers and Mid North Coast are expected to see "widespread, high rainfall totals" exceeding 100mm, she said.
Late on Saturday, the Insurance Council of Australia declared an insurance catastrophe for southeast Queensland, with claims and assessment teams to begin helping householders as soon as it is safe to do so.
The federal government says disaster assistance has been activated for 10 local councils in Queensland's southeast.
AAP with The Project