Victoria, Tasmania and NSW continue to take the brunt of the rain with residents evacuated as flood waters continue to rise.
Here is a snapshot of how things are looking across the three states:
Victorian communities remain on high alert for dangerous flooding, with residents in six towns urged to leave homes and get to higher ground.
Evacuation orders are in place for Rochester along the Campaspe River, Carisbrook near Maryborough and Seymour on the Goulburn River
Residents have also been instructed to leave at Maribyrnong on the Maribyrnong River, the city of Benalla on the Broken River and at Wedderburn following a breach at Skinners Flat Reservoir.
Strong, fast moving water from the dam a metre deep was expected to course through Wedderburn township via the Calder Highway, authorities said on Friday morning.
People in Rochester were told to abandon homes as floodwaters rapidly rose and were likely to inundate the area from early Friday. The Campaspe was slated to peak in the afternoon.
Emergency relief centres have been set up close to Rochester, Carisbrook and Seymour.
Those along the Campaspe from Lake Eppalock to Barnadown have also been advised to get to higher ground, while an emergency warning has been issued for Seven Creeks to Euroa.
Watch and act alerts urging people to stay indoors are widespread across Victoria.
Areas north of the Great Dividing Range were among the heaviest hit by the rain through Wednesday and Thursday and more central areas also saw significant falls, according to the Bureau of Meteorology.
Between 9am and 6pm on Thursday, Pyalong recorded 62 millimetres and Avalon Station saw 60mm.
While Strathbogie North also recorded a 58mm dump on Thursday, it had copped 187mm since Wednesday morning.
The big wet was starting to clear out of western Victoria on Thursday night and forecasters predict conditions will improve for the state's central parts and then into the east on Friday.
Despite this, volumes of water are yet to make their way downstream through river systems.
Earlier on Thursday, Victorian SES Chief Operations Officer Tim Wiebusch said Seymour was facing its highest flood level since 1974.
There was potential for 187 properties to be inundated and a further 279 to be isolated, he told reporters.
Authorities expected up to 700 properties in Rochester to be isolated by Friday and Shepparton to experience its worst flood in almost three decades on Saturday afternoon, with up to 600 properties isolated.
The bureau warned of damaging winds over elevated areas in the state's central and eastern parts but they were expected to clear eastwards on Thursday evening.
Rain will ease across NSW as a cold front heads away from the east coast with clear skies to begin appearing by the weekend.
Yet the Bureau of Meteorology warns southern inland NSW should remain alert for flash flooding.
Hundreds of people were ordered by the State Emergency Service on Thursday to evacuate parts of Forbes in central western NSW by 8pm before major flooding hit the area.
The Lachlan River was expected to reach a major flood peak of 10.6 metres later on Thursday or early on Friday, prompting the emergency warnings for Forbes.
Moderate flooding also affected Wagga Wagga after the Murrumbidgee River peaked on Thursday morning.
A deep low-pressure system is combining with a deep tropical air mass, and forecast to produce areas of heavy rainfall over southern parts of the Lower Western and Riverina Districts, and onto the western slopes of the Alpine region overnight.
The system will also bring gusty alpine winds.
Flood warnings are current for catchments across southern NSW. Locations which may be affected include Albury, Tumbarumba, Deniliquin, Hay, Broken Hill, Wentworth and Balranald.
Although clear skies are on the horizon, the fortnight ahead will be soggy with above-median rainfall (greater than 80 per cent chance) on the cards for large parts of the eastern two-thirds of Australia.
People in Tasmania's flooded north and northwest have been warned there is still a long way to go before rivers and catchments reach their peak.
Evacuations orders were issued on Thursday evening for communities along sections of the swollen Mersey and Meander rivers in the state's northwest.
Intense heavy rain that began on Wednesday night is expected to ease in the early hours of Friday, but authorities are urging people to stay on high alert.
Bureau of Meteorology forecaster Paul Fox-Hughes said rainfall would ramp up on Thursday evening as a secondary low pressure system moved past Tasmania.
The Great Lakes area in the state's central north topped the rainfall tally with 220 millimetres in a 24-hour window, while records were broken in several locations.
Authorities have warned river peaks in some parts could reach levels seen in mid-2016 when flooding claimed the lives of three people and caused $180 million worth of damage.
Five people and their animals were rescued from a property at Liffey, southwest of Launceston, on Thursday, while the SES has received more than 100 calls for assistance.
Tasmania Police has urged people to avoid travelling unnecessarily and to not drive through floodwaters.
- Australian Associated Press