The worst-affected areas were in the Midlands, where roads flooded, rail passengers were stranded and many schools closed.
About 50 Environment Agency flood warnings - meaning "immediate action required" - are currently in place.
More than 160 lower-level flood alerts have been issued across much of England and parts of Wales.
Flooding continues to cause severe disruption on some roads, including sections of the A428 and A3400 in Warwickshire.
BBC forecaster Tomasz Schafernaker said Thursday's weather would be a "lot quieter", with "none of that heavy rain that we had first thing in the morning on Wednesday".
He said cloud would clear overnight, leaving a "few spots of rain" in central and eastern England by Thursday morning, with clear skies and low temperatures elsewhere.
On Wednesday, British Transport Police formed human barriers to hold back crowds at London Euston after trains between Rugby and Milton Keynes were cancelled.
In Warwickshire, 14 schools were closed and a number of people were rescued from cars by firefighters due to floodwater.
In Birmingham, a man was filmed using a ladder as a bridge to reach a van which was stranded.
Dozens of flood warnings remain in place in central England following heavy rain and disruption on Wednesday.