Bureau of Meteorology senior forecaster Richard Carlyon said there was a warning for flash flooding in the region

"The higher rainfall totals are in the southern Mallee and northern Wimmera," he said.

"It could lead to flash flooding and the rainfall rates could be quite high because it's a fairly humid weather system.

"We're forecasting totals of 20mm to 40mm of rain over the northern Wimmera and 10mm to 20mm further to the south and south-west. 

"Horsham is in the 20mm to 40mm range."

Mr Carlyon said the rain would increase during Thursday morning.

"There's been a bit of light rain across the Wimmera on Wednesday," he said.

"Those falls will increased Thursday morning as heavier rain moves down from the north-west during late morning, early afternoon and into the evening."

The bureau has also warned of the potential for landslides and debris on roads in fire-affected areas of the Grampians.