Residents in parts of both states could be cut off, with more than 100 roads already swallowed by rising waters in Queensland.
The town of Clermont in Central Queensland recorded 169mm since 9am yesterday.
The rainy conditions, which stretch for thousands of kilometres across northern and eastern Australia, are expected to linger for about a week.
Sydney was hit by another intense storm late yesterday, leading to flash flooding.
The air mass will also see continued rainfall across a soaked NSW.
Minor flooding is possible in the Hawkesbury Nepean region this afternoon, which was hit hard earlier this year.
There are also renewed flood fears for Gunnedah and Forbes, where floodwaters recently swept over farmland, devastating crops.
A sudden storm in Sydney yesterday saw roads inundated, with cars driving through heavy water in Enmore.
Sydney is set for up to 45mm of rain today, with lighter falls expected tomorrow and Sunday.
Brisbane too will see its heaviest rain today, with up to 50mm predicted and a storm likely.
The BoM declared a La Niña has developed in the Pacific Ocean, leading to wetter than normal periods for eastern, northern and central parts of the nation.
La Niña often brings above-average rainfall, cloud cover and cooler temperatures.