Emergency services have worked late into the night to try to clear the water from roads and railway lines in Todmorden in West Yorkshire.
Parts of the market town were left under one and half feet of water.
Police have asked people to avoid areas that were badly affected and said that waves from driving through the water can damage houses.
They have also issued a warning for people not to cross a bridge in the town they believe may have been damaged.
I have just spoken to the abattoir owner in Yorkshire. He says it is a complete surprise the FSA have visited his site. The owner says he has a license to slaughter horses and denies any wrong-doing.
Britain is bracing for yet more wet weather, as bands of heavy rain move across the country.
This video, shot by Robert Pickering, appears to show a tornado last night over Todmorden, near Manchester.