Norman Goldstone, chairman of Childwall Hebrew Congregation, said a caretakers' team had spent five hours clearing water out of affected areas, and that the main shul, offices and bet hamedrash were undamaged.
He said: "It's not the end of the world. The inside ceilings have caved in but it's not going to close the shul. We've got a team coming next week to clear away the rubble that fell from the ceilings."
Stapely Jewish Care Home was unaffected, despite flooding in nearby streets. Staff at King David High School reported long delays to get home, but pupils were unaffected.
Merseyside police and the city council reported major routes such as Allerton Road and Queens Drive in Childwall, near to Liverpool's Jewish community, were cut off by flood waters.