Severe flood warnings are in place in Shrewsbury and Ironbridge, meaning there is a danger to life.
Shropshire Council closed many routes into and around Shrewsbury, and said flooding could seal off the centre.
The Environment Agency (EA) said 40-50mm of rainfall Welsh mountains was expected to cause problems further down the River Severn.
There are currently dozens of flood warnings and alerts in England after heavy rainfall.
Defences went up in Frankwell and Coleham Head in Shrewsbury overnight. The EA has also issued a severe flood warning for the Wharfage, Ironbridge.
It warned properties there would be affected by flooding due to temporary defences “overtopping” following persistent heavy rainfall.
Debbie Bradbury-Walker, who lives near the English Bridge with her partner Anna, said water had entered their house.
“We have [an] 8ft cellar which is a godsend as that’s all been filled,” she said.
“There is about three to four inches of water in the house on the ground floor.
“It’s the first time it’s flooded like this and entered the house in the five years we’ve lived here. The drains are full but luckily we still have electricity at the moment.
“We have a way to escape from the house if we need. The rear is built up.”
Chris Bainger, from the EA, said they were predicting a water level of 4.8m (15.7ft) to 5.2m (17ft).
“If we reach that [higher] level… then we’re above the highest that we’ve ever had,” he said.
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Shropshire Council said businesses were open in Shrewsbury, but people could only reach the centre on foot.
Clive Wright, from the council, said staff were out overnight warning residents at risk of flooding.
“The river levels are set to rise during the day so we do expect that at some point today we may get more flooding and if the barriers breach at Coleham again, as they did last week, then that will close off the town and the English Bridge,” he said.
In the last week of October 2000, the Severn rose to its highest level for over 50 years, flooding Shrewsbury, Ironbridge and Bridgnorth.
Erica Jones, who runs Coleham Sandwich Bar & Deli in Shrewsbury, said they were “staying open as long as we can”, after being “very lucky” last week.
She said: “It got to about six inches from our door.”
Carol Calcutt, who lives close to the river, said: “I’m very worried. Looking out of my window now the water really is coming up in kind of small waves. It is moving very quickly again.”
Telford & Wrekin Council workers have spent the night distributing sand bags in the Ironbridge area. Homes that are at risk in Jackfield were the first to receive help.
Scattered showers are expected across the Midlands later.
Shrewsbury Colleges Group said its English Bridge and Welsh Bridge campuses were closed on Monday, but its London Road campus would be open as usual.
Shrewsbury High School said its senior school would also be closed, although the prep school would be open without a school minibus service.
Coleham Primary School said it was planning to be open as normal. But Coalbrookdale and Ironbridge Church of England primary school was shut.
Last week homes and businesses were affected by floods in the wake of downpours brought by Storm Dennis.
The Rivers Wye and Severn reached their highest-ever levels.
