A couple has woken to ankle-deep water inside their home as flash flooding inundates towns across regional Victoria.

Some areas were inundated with their highest daily rainfall ever recorded and some were ordered to evacuate as floodwaters rose on Monday night.

Daniel and Rhiannan Drake lost their home at Goornong, north of Bendigo, made it out with just a few possessions and their beloved pets.

“I woke up to my wife screaming ’cause she’d put her foot out of the bed and it was wet,” Daniel Drake told 9News.

“It was halfway up our shin throughout the house.”

The couple were rescued by water police during the night.

“We put all our belongings that we had and our cats on that and we took the boat out,” he said.

Evacuation orders remained in place on Monday night in the towns of Seymour and Rochester as riverine floodwaters rapidly rose, while Yea residents were told it was too late to leave and that they must shelter at the highest point possible.

The Victorian SES said as of 3pm it had received over 1200 requests for assistance since 7am Monday, including 38 water rescues.

The SES carried out 38 swift water rescues; 16 in the Bendigo area, eight around Goornong, four at Heathcote, two at Lockwood and two at Woodvale.

“In the majority of cases it’s people taking their lives in their own hands and attempting to drive through flash floodwaters,” SES chief officer operations Tim Wiebusch said.

“We cannot emphasise enough, do not attempt to drive through floodwaters it could be the last decision you make,” he added.

Earlier, Heathcote in central Victoria was hit with a staggering 184mm of rain in the 24 hours to 9am, Bureau of Meteorology senior meteorologist Michael Efron said, which is equivalent to about three months of rain.

“That’s a daily record for any month, with over 120 years of data,” Efron said.

Nearby, Redesdale was hit with 117mm of rain in the same period, Rochester received 125mm of rain and Bendigo received 92mm.

Efron said these figures all marked the highest daily rainfall ever recorded in the areas in more than 120 years.

The Bureau of Meteorology issued a severe weather warning for Bendigo, Shepparton, Seymour, Kyneton, Wodonga and Wangaratta this morning after extreme weather swept parts of northern and southern Victoria overnight.

Across the state, there are widespread road closures, with numerous homes also affected.

“The focus will shift in the next few hours from flash flooding to riverine flooding,” Wiebusch warned this afternoon.

Flooding is expected in Wangaratta and Shepparton in the state’s north mid-week, Emergency Management Commissioner Rick Nugent warned.

Just before midday, an evacuation was ordered for Seymour in the Shire of Mitchell, with major flooding expected to break 1993 flood record levels.

In an update, VicEmergency warned flooding above the floor level of a single-storey home was likely to occur and access to key roads would be impacted.

A watch and act warning was issued for Campaspe River from Lake Eppalock to Barnadown,with river levels expected to reach around 6.50 metres – above the November 2010 flood level.

“Act now – take actions immediately to protect your life and property, and move to higher ground,” the notice reads.