Lincoln could gather strength and redevelop into a tropical cyclone again, as communities in its path prepare for heavy rainfall and flooding.
The weather system is barrelling towards Western Australia and should cross the border near Halls Creek as it tracks towards the coast.
"The ex-tropical cyclone will move west-northwest through the Kimberley, driving areas of heavy rainfall, stronger winds and flash flooding with it," the Bureau of Meteorology's Miriam Bradbury said on Monday.
"It's likely to cross off the Kimberley coast late Wednesday going into Thursday."
The low is expected to move south down the coast late in the week.
"As it moves over those warm waters it's likely to increase its energy and its power and there is actually a high chance it may strengthen back to tropical cyclone intensity at this point in the week," Ms Bradbury said.
"That means even heavier rainfall and stronger winds that may impact some coastal parts of Western Australia."
The bureau said it was possible ex-Cyclone Lincoln could cross the coast near Exmouth at the weekend as a severe tropical cyclone.
The system has bucketed heavy rain in the Northern Territory, with 24-hour totals over 100mm recorded in some areas.
A severe weather warning is in place from Lajamanu to Halls Creek, with six hourly rainfall totals over 100mm and flash flooding possible.
"So much rainfall coming down in such a short space of time can cause your property damage, and can quickly impact roads and access routes as well making them muddy or impossible," Ms Bradbury said.
The northern Tanami and the southern Gregory Districts in the NT should prepare for potential flash flooding on Monday and Tuesday.
A flood watch is in place for parts of Bonaparte coastal rivers, Carpentaria coastal rivers and central inland rivers in the NT.
It extends into WA's Kimberley region and also takes in the Fitzroy Rivers and Sturt Creek district.
Catchments in these areas are already wet because of rain over recent weeks and are likely to respond quickly to further heavy falls, the bureau said.
Isolated heavy fall totals up to 200mm possible across the flood watch area over the next two days.
Major flood warnings also remain in place for Queensland's far northwest.
The saturated region that was hit by ex-cyclone Kirrily in January faces a renewed flooding threat.
"Even though the ex-tropical cyclone has moved westwards now and that risk of heavy rainfall is easing we still could see high flows from past rain events moving through these Queensland catchments causing further flood warnings over the coming days," Ms Bradbury said.
Heavy rainfall in the region caused by ex-cyclone Lincoln has triggered warnings for the Diamantina, Nicholson and Flinders rivers.
Major flooding is continuing on the Nicholson River at Burketown and the airstrip is expected to be cut off over coming days as thunderstorms hit the region again.
A flood peak was forecast at the Diamantina River at Birdsville on Sunday night and is expected to continue falling over coming days.
