Some people were forced to leave their homes during Saturday night's deluge in Poynton, while a landslide affected the train line between Stockport to Disley.
Firefighters used rescue boats to help move people to a temporary emergency centre.
The waters have now subsided, but several roads remain closed.
The floods, caused by heavy rain throughout Saturday, left many homes damaged and 15 properties Offerton's Sheerwater Road Estate were hit by power cuts.
Both Greater Manchester and Cheshire fire services said there were no casualties.
Middlewood Road in Poynton was expected remain closed until Monday morning.
The Stockport to Disley railway line had also yet to reopen.
A spokesman for Cheshire East Council said: "While we were prepared for extreme weather conditions, no one could have predicted the severity of flash flooding that we experienced.
"More rain is expected in the next day or so and we are continuing to monitor the situation on behalf of our residents."
A clean-up operation is under way after flash floods caused widespread disruption across parts of Greater Manchester and Cheshire.