Downpours had as many as 151 flood warnings and advisories in effect early in the day, and about 450 people had been evacuated due to rising water in Lancashire.
"We're asking people in Greater Manchester, Liverpool, the Wirral, North Cheshire and Lancashire to remain vigilant and prepared for flooding," a spokesman for the Environment Agency told The Daily Telegraph.
The newspaper said thousands of homes and businesses were threatened but were remaining out of harm's way thanks to levees and other defenses.
Also hard hit was the annual Isle of Wright music festival, where fans slogged through countless puddles and hundreds of cars became stuck in the deep mud. Train service and several other outdoor events were delayed or canceled due to the weather, which was expected to ease up Sunday.
"We've seen unprecedented wet weather during June and the catchments, the soil, is all sodden and this last heavy bout of rainfall has landed on top of that soil and quickly gone down into rivers and is now going down through the Pennine Rivers," the Environment Agency's flood risk manager told the BBC, referring to the Pennine mountain chain, sometimes called the backbone of England.