The Environment Agency has issued 17 warnings, meaning “flooding is expected – immediate action required”.
And it has put out another 24 alerts, which mean “flooding is possible – be prepared”.
The warnings – mostly for northern parts of England – come at the end of another day of heavy rain.
Parts of Britain were hit with up to a month’s worth of rain today as thunderstorms battered the nation.
It followed even more showers on Monday and Tuesday, sending water levels soaring.
And following the latest deluge of rain, areas are now under flood watch as the shower pour into rivers.
The 17 warnings are in place from as far south as Leicestershire, through Derbyshire and Cheshire, to Greater Manchester and Yorkshire.
The alerts, along with the warnings, mostly cover an area of north and north-east England.
The Met Office had issued an all day yellow warning of heavy rain and thunderstorms earlier today, covering a large swathe of England northwards from Manchester, Sheffield and Lincoln.
In Gringley on the Hill in Nottinghamshire, 11.6mm of rain fell in the hour up until 2pm on Wednesday, the Met Office said.
At High Mowthorpe in North Yorkshire, a total of 40.2mm fell in the 12 hours up until 2pm.
The army was drafted to help with damage after storms even left scores of homes and businesses flooded and roads and bridges washed away.
Soldiers from 2 Yorks arrived in Grinton, North Yorkshire, after parts of the region had up to 82.2mm of rain in 24 hours on Tuesday.
One 75-year-old woman described how she almost drowned when her pub, the Red Lion Inn, in Langthwaite, Richmond, North Yorkshire was filled by 5ft high water on Tuesday night.
Rowena Hutchinson told PA on Wednesday how the flood water came gushing into the pub “like a waterfall”, leaving her under the water up to her chin.
Describing the torrential rain that ruined her home she said: “It’s completely smashed doors off, and a wall has gone.
“The speed and force of the water was unbelievable, it’s just tossed the doors all over the place.”
Rescuers reported seeing sheds and oil tanks floating down roads as “100 or more” homes in the Yorkshire Dales were deluged on Tuesday.
Fire authorities received around 115 calls to flooding incidents in Leyburn and Reeth in the Yorkshire Dales on Tuesday evening, while pictures and videos from the nearby village of Cogden Gill showed a bridge used in the 2014 Tour de France in ruins.
Organisers for the Ard Rock mountain bike event, which was due to take place in Reeth from Thursday to Sunday, said it had been cancelled.
Train passengers also faced disruption after a landslip between Carlisle and Skipton.
Speaking on Wednesday, Met Office forecaster Helen Roberts said the parts of England had been hit by “a significant amount of rainfall in one day”.
She added: “The heavy showers will continue for a good few hours yet across the northern half of the UK.”
Roberts said showers were expected to ease by the end of Wednesday, leading into a dry night.
Further showers are due on Thursday but they are not expected to be as heavy, with no weather warnings currently in place.