A tropical cyclone will hit Queensland this weekend, and rain and flooding will affect New South Wales, South Australia, Victoria and Tasmania as extreme weather sweeps over nearly all of eastern Australia.

The Bureau of Meteorology has declared two simultaneous extreme weather systems on the east coast – a rare event that will create thunderstorms from Queensland to Tasmania.

Tropical Cyclone Owen is picking up strength in the Gulf of Carpentaria, and was upgraded to a category two storm on Wednesday afternoon. It is expected to reach category three by Thursday morning. On Friday it will move east into Queensland, bringing heavy rain and strong winds.

In Victoria, an extreme low pressure system is forming that will bring storms and floods to the southern part of the country at the same time.

Grace Legge, the bureau’s extreme weather forecaster, said the rain would begin on Wednesday. “We are seeing severe thunderstorms all the way up from the north-west parts of South Australia through to the south-east, through Victoria, and into eastern NSW.”

The rain might ease in intensity on Thursday but could spread in area, reaching the northern tip of Tasmania. “It’s hard to say whether we will get those heavier falls but we could be getting flash flooding too,” she said.

On Wednesday, James Taylor, the manager of the bureau’s extreme weather desk, said some north-western parts of the state could have their wettest day of the year.

The bureau is predicting between 30mm and 100mm of rain in the region across Wednesday and Thursday. Legge warned residents not to drive through flood water, and said there was also the possibility of hail in South Australia.

Brisbane is forecast to experience rain from Thursday to Monday – with up to 50mm on Friday. Sydney will get showers from Thursday to Saturday, and Melbourne is expected to face storms from Wednesday to Sunday, with the potential for thunderstorms and 45mm of rain on Thursday.

In the north, Cyclone Owen was judged a category-one storm at 7am on Wednesday as it hovered 215km off the coast of Borroloola in the Northern Territory.

The bureau has predicted that it could bring 110km/h gale winds between Cape Shield and the border with Queensland on Wednesday. On Thursday those winds could extend to Burketown and Mornington Island. Residents have been advised to immediately take shelter and close businesses.