The weather system is located near Lajamanu in the Northern Territory and is heading west towards WA's Kimberley region.
It should reach the WA/NT border later on Monday, moving into the northern parts of the Kimberley in the coming days.
"The risk of rain is ongoing so we have flood watches covering pretty much all of central Northern Territory and the Kimberley as well so that's really just indicating that we do expect to see river rises in response to the rainfall," the Bureau of Meteorology's Miriam Bradbury said.
⚠️ A Severe Weather Warning is current in the — Bureau of Meteorology, Australia (@BOM_au) #NT for heavy rain and strong winds from ex-TC Lincoln. This warning area is likely to extend into #WA later todayFlood Watches & Warnings are current across northern Aus. Some roads are restricted. Latest: https://t.co/jlOoTZL1iF pic.twitter.com/1NuijWQIVrFebruary 18, 2024
Barkly, northern Tanami and the southern Gregory Districts like Kalkarindji in the NT should prepare for potential flash flooding on Monday.
The bureau has warned that roads, access routes and supply chains may be cut off by floodwaters.
Rabbits Flat recorded 104mm in the 24 hours to 9am while Tennant Creek was hit by another 58mm on top of the 100mm over the weekend.
Across the western region on Monday, six-hourly rainfall totals of 60 to 100mm are forecast with 24-hour totals between 80 and 140mm.
The rain is set to worsen on Monday night with totals up to 150mm over six hours near the centre of the system and 220mm over 24 hours.
The tropical low is not just bringing heavy rainfall.
Strong winds are hitting the regions with gusts of up to 90km/h.
Ms Bradbury said as the ex-cyclone moves into northern WA, communities should prepare for the risk of flooding in coming days.
"The catchments are highly sensitive to any rainfall given the significant rain we've seen not just over recent months with the monsoon but also over the last couple of years," she said.
The Kimberley was hit by destructive flooding in January 2023 with water levels cutting off communities and destroying essential infrastructure.
"There is a lot of damage and clean up recovery still happening," Ms Bradbury said.
The Kimberley faces weather warnings after the region was badly damaged by floods about a year ago. (HANDOUT/ANDREA MYERS)
The ex-cyclone should reach WA's coast by mid-week.
Although ex-cyclone Lincoln is tracking towards WA, major flood warnings remain for Queensland's far north west.
The saturated region that was hit by ex-cyclone Kirrily in January faces a renewed flooding threat.
Heavy rainfall in the region caused by ex-cyclone Lincoln has triggered warnings for the Diamantina, Nicholson and Flinders rivers.
Ms Bradbury said a number of communities in the region were still isolated but it may take weeks for floodwaters to subside.
"A lot of the rivers across western Queensland are slow moving, the flood peaks can take not just days but sometimes weeks to move through," she said.
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.
Ms Bradbury said rain was mostly easing in the far north west, allowing some recovery and clean up efforts to start.
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