The troughs are passing over each other causing the wild weather in Queensland's south and northern NSW, the Bureau of Meteorology says.
Rainfall totals up to 200mm are forecast across both states in coming days.
Residents in an already sodden Queensland are being told to prepare for flash flooding.
The Darling Downs, Granite Belt and Maranoa in Queensland's southwest are forecast to get thunderstorm activity on Thursday with widespread rainfall totals between 20mm and 50mm.
Isolated falls that increase the risk of flooding could be up to 100mm in towns from Charleville to Goondiwindi and over to the Gold Coast.
Severe Weather Update: Heavy rain for large parts of — Bureau of Meteorology, Australia (@BOM_au) #NSW and southern #Qld this week. Video current: 11am AEDT 3 April 2024.Latest forecasts and warnings: https://t.co/4W35o8iFmh or the BOM Weather app. pic.twitter.com/5dkRoV2tLtApril 3, 2024
A flood watch has been issued for dozens of catchments across the state's southwest including the Paroo River, Wallam and Mungallala Creeks and Moonie River.
The bureau said floodwaters could rise on Thursday night.
For residents near the Moonie and Condamine rivers it marks just a few months since river levels rose, flooding homes in a January emergency.
The weather system will move south into northern NSW developing into a low pressure system, bringing widespread rain of 30mm to 50mm and up to 100mm in some areas.
The bureau's Miriam Bradbury warned the weather system will bring severe storms with heavy rain, strong winds and high sea swells.
"As a trough deepens off the coast of east coast NSW it is likely to drag in further moisture and direct it across eastern and central NSW with the risk of heavy falls becoming more widespread an intense," she said on Wednesday.
The New England and Northern Rivers regions are anticipating the first wave of wild weather before the system tracks further south to the Hunter, Sydney, Blue Mountains and Illawarra on Friday.
NSW State Emergency Services are preparing for the worst with residents urged to get ready for the storms.
"Flood and storms teams are on standby to respond should they be required, but we're pleading with the community to be prepared, stay informed and not drive through floodwaters," assistant commissioner Sean Keans said.
A flood watch is in place for the Mid North Coast, Sydney region, South Coast and parts of the north west.
Major flooding is possible on the Hawkesbury Nepean River from Friday.
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