The evacuation began at 3am and went on all night.
Michal made the decision to leave his home in the Karlin area of the city after the evening television news reported that it could be inundated by a metre of water.
He and his wife Marie put their three children to bed and stayed up all night moving as many valuable possessions as possible upstairs.
As they did so elderly neighbours were leaving in specially provided buses.
Police going from door-to-door arrived at their flat at 6am to make sure they would be leaving soon.
"There was no panic, but some people were angry because they didn't want to leave," Michal said.
Lights out
"I felt that people didn't believe that the flood will hit them."
Michal and his family - confident that the wave would not arrive until 2pm - may have been among the last to leave.
"When we left at 6am it was still dark, but there were no lights on in the surrounding buildings," he said.
They took a few clothes and belongings and travelled by underground to Michal's parents' house.
Now they can only wait, and hope that the damage is limited.
Prayers
"I am praying," said Michal.
"I have a big library, 2,000 or 3,000 books, which I could not save. It includes philosophy, and Czech history - it is a lifetime's collection."
About 25,000 people were evacuated from the Karlin district.
Those with no relatives to visit have been housed in schools, some of which have closed.
Officials have said it could be five or six days before they are able to return home.