The order gives Bush power to evacuate residents and send resources and personnel to help city and county governments.
Bush declared emergencies in Collier, Lee, Charlotte, Hardee, DeSoto, Sarasota and Manatee counties, which were hit with as much as 21 inches of rain in the last several days.
About 40 homes in Sarasota County were flooded, and storms did $2 million in damage to seawalls in Punta Gorda Isles in Charlotte County.
The state also asked residents to evacuate 850 homes in low-lying subdivisions near Myakka River in southern Sarasota County. Officials did not know late Tuesday how many homes had been evacuated.
Heavy rains again hit southwestern Florida on Tuesday before tapering off.
Meanwhile, disaster assessment teams found little damage near Lake Manatee, where heavy rains had threatened to cause a dam to overflow Sunday.