About 100mm of rain could fall on the Border in just two days as a low pressure trough creates a humidity and storms says the Bureau of Meteorology.
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Senior forecaster Richard Carlyon said the North East would bear the brunt of the state's thunderstorms in coming days, with a severe weather warning issued for the region.
"It looks like the bullseye of the rainfall will be towards the north east of Victoria where we [have issued] a severe weather warning for heavy rain for the north east, parts of the north central and northern country," he said.
"It looks like they'll will be in the firing line of heavy rain.
"The two day total around Albury-Wodonga could exceed 100mm."
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Mr Carlyon said falls of between 20 and 60mm were expected on Wednesday, and falls up to 80mm were expected in the North East on Thursday.
The bureau's severe weather warning cautioned that heavy rainfall could lead to flash flooding in the afternoon or evening.
Mr Carlyon said a weather system, known as ex-cyclone Esther, was drifting southwards across northern Australia causing the stormy weather.
"As it moves southwards it will pump moisture over a low pressure trough over Victoria so we're likely to see very humid conditions develop over Wednesday and Thursday and also rain develop across the [Victoria] during those days," he said.
Temperatures are predicted to drop to a low of 17 degrees on Wednesday with a maximum of 23 expected. On Thursday temperatures will be marginally higher with the bureau forecasting a low of 18 degrees and a high of 24. By Friday the rain will mostly have moved away from the North East and temperatures are forecast to increase to a maximum of 29 degrees.