The Katherine River reached a predicted peak of 19.2 metres on Saturday night at Katherine Bridge, on the outskirts of the Northern Territory town of about 6000 people.
The high water mark is above the bridge deck and around the same level as 2006 floods.
Authorities are warning more rain is to come as hundreds of residents in remote communities are evacuated.
Chief Minister Lia Finocchiaro reported all residents had been evacuated from the flood-hit Aboriginal community of Palumpa, south of Darwin.
Evacuations had also taken place in the Daly River community, where 208 people have been moved to safety, with around 70 residents deciding to stay.
It's the second time in as many months that residents from Daly River have been evacuated due to rising flood waters.
At Beswick, east of Katherine, residents from Bottom Camp have been relocated to Top Camp as a precaution due to rising water levels.
The evacuation operation involved 13 helicopters, while about 500 people were sheltering in evacuation centres in and around Katherine, Ms Finocchiaro said.
In the Katherine region, both the Stuart and Victoria highways are closed due to flooding.
Katherine resident Trent de With used his business social media account to share first-hand accounts of the flooding on Saturday afternoon.
"It's just slowly creeping now," he said of the rising river on the Rod and Rifle Tackleworld Katherine Facebook page.
"It's creeping into the street and so many of our friends and families up in the north side of town, yeah you've lost houses, heaps of belongings.
"I feel for you and we'll be ready for you when you need to clean up ... you've got a community behind you."
On Sunday morning, he posted another video showing flood waters receding at Katherine Bridge.
Just before 4am, the Bureau of Meteorology cancelled a severe weather warning for people in the Daly and Arnhem districts.
The area had been lashed with heavy rain, including more than 155mm at Theyona Station, on the Daly River, in a six-hour period to mid-Saturday afternoon.
As the Northern Territory cops a drenching, almost all of Queensland's coastline is under flood alert as a tropical low moves inland.
The Herbert and Daintree rivers in the north of the state are continuing to flood after massive rainfall in the last 24 hours, Bureau of Meteorology senior meteorologist Dean Narramore said.
Alligator Flats, near Gladstone, recorded 212mm while most of northern inland Queensland saw falls of between 50 and 150mm.
There was little short-term relief in sight as most of the state should prepare for the soaking to continue, Mr Narramore said.
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