Thirty nine flood warnings are in force in West Yorkshire on the rivers Calder, Colne and Spen due to heavy rainfall, the Environment Agency says.
Flood sirens were sounded at 19:30 BST on Friday in Hebden Bridge and Todmorden to warn of imminent flooding.
West Yorkshire fire service said it was responding to a "very high" number of flood calls, especially in Todmorden.
The service is only responding to "life-threatening" incidents, it said.
BBC reporter Dan Johnson, speaking from Mytholmroyd, said the River Calder had burst its banks in the town centre - flooding businesses and homes.
He said there was 2ft (0.6m) of water in the main street and the fire service was using inflatable boats.
Guest house owners David and Sally Henry, who run their business in Hebden Bridge, said they "were ruined" after flood waters and sewage affected their property.
"I put sandbags on the at-risk doors but the water was three or four feet deep within minutes and it started coming through the doors," Mr Henry said.
"Then the sanitary waste came firing out because of the pressure in the drains.
"It will take at least six months to clean this up, everything's contaminated.
"I think we're both a little bit in shock, we don't know how to move forward as it's the weekend we can't get in touch with [insurance] people."
Wakefield MP Mary Creagh, Labour's shadow Environment Secretary, said emergency services had worked well, but she was worried about people getting flood insurance in the future.
"The North of England is starting the big flood clean up and crossing its fingers for the next 24 hours," she said.
"I pay tribute to our police, fire and council staff who have worked through the night helping communities deal with the misery and disruption of the floods.
"People in flood-prone areas are finding it harder to get insurance and their premiums and excesses are going up".
The Calder Valley railway line, between Leeds and Manchester Victoria, has been affected by flooding and trains have been stopped on the route, a Northern Rail spokesperson said.
'Landslip and flooding'
Martin Driver from Metro, the organisation that looks after West Yorkshire's buses and trains, said there had been disruption to services.
He said: "There's been a landslip and flooding near Walsden [near Todmorden] so there's buses replacing trains over the tops between Rochdale and Halifax.
"But passengers can travel to Manchester Piccadilly on TransPennine trains."
Mr Driver said there was flooding at Lock Lane in Castleford that had affected bus services.
Trains between Wakefield Westgate and Leeds have also been affected.
Travellers are advised to check with National Rail Enquiries before travelling.
Flood warnings on the River Calder include Hebden Bridge, Liversedge, Mirfield, Mytholmroyd, Todmorden and Wakefield.
Flood warnings on the River Colne include Huddersfield and Slaithwaite.
Flood warnings on the River Spen include Horbury Junction and Mytholmroyd.
The Environment Agency said the forecast may mean some "respite" from rain on Saturday but further rain was forecast for later in the weekend.
The Met Office has issued severe weather warnings for rain affecting North West England, East Midlands, Yorkshire and Humber, West Midlands, Northern Ireland, South West Scotland Lothian Borders, Strathclyde, Central, Tayside and Fife, and Wales.
The sirens in upper Calderdale have been installed in addition to the agency's Floodline Warnings Direct service.
There are eight sirens, which sound like an air-raid siren, in the area.