The trough began generating very warm winds and storms over northern WA, the Top End, Queensland and NSW on Thursday, bringing extreme humidity, rainfall and thunderstorms on Friday.
Wild weather lashed southeast Queensland and northern NSW earlier this week, causing flooding and damage to beaches.
The rain is expected to continue to pour in both states on Friday and linger over southeast QLD and northern NSW until at least next week.
In Queensland, there is a severe thunderstorm warning in place for St George, Bollon, Mitchell, Dirranbandi, Carnarvon National Park, Mungindi and Glenorie.
Final flood warnings are also in place for the Burrum and Cherwell River Catchments and the Nerang and Coomera Rivers.
In NSW, strong wind warnings have been issued for Sydney, Illawarra, Batemans, Eden, Macquarie, and Hunter regions.
A severe thunderstorm warning is in place for Coffs Harbour, Port Macquarie, Taree, Armidale, Tamworth and Moree.
Tweed and Wilsons Rivers have final flood warnings and minor flood warnings have been issued for the Orara, Gwydir and Richmond Rivers.
The Bureau of Meteorology (BOM) is concerned that saturated grounds in the north could lead to riverine and flash flooding over the next few days.
"The prime concern is flash flooding," meteorologist Helen Reid said on Friday.
"Some of these thunderstorms can be quite intense and with so much moisture in the air it can come down all at once with a severe thunderstorm."
The NSW State Emergency Service asked people to move their cars under cover and avoid floodwaters, secure loose items around their homes and keep at least eight metres away from fallen power lines.
The SES has responded to more than 2300 requests for assistance across NSW over the past eight days.
Over the border in Queensland, Gold Coast beaches will reopen on a case-by-case basis on Friday after being closed on Thursday for council workers to clear washed-up debris.
Australia weather: Cyclones may form in the north
The Northern Territory will possibly see thunderstorms for the next seven days as meteorologists keep an eye out for any cyclones forming, BOM meteorology Claire Yeo said.
“It’s an evolving situation,” she said.
Ms Yeo said the area will see widespread rainfall, with inland expected to record 50 to 100mm over three days.
Coastal areas should see 200 to 300mm during the same time frame.
Ms Yeo warned NT residents to keep an eye on weather forecasts and any information from their local emergency services.
A front brought showers to Melbourne and Tasmania on Friday but will clear up for the weekend.
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