Officials ferried people by boat from homes in DeBary, 25 miles north of Orlando, where some streets were under 4 feet of water, and flooded neighborhoods in and around Tallahassee.
"The water is very deep. It's already at everybody's door," said Debra Galloway, who lives in the Timber Lake subdivision east of Tallahassee. She was still at home Sunday evening but had no power and said if the rain continued, she would join neighbors who had already left by boat.
Fay made landfall a record four times in Florida before it was downgraded to a tropical depression late Saturday. The storm caused widespread flooding as it zigzagged across Florida for nearly a week.
Fay has been blamed for 13 deaths in the U.S., 11 in Florida and one each in Alabama and Georgia. A total of 23 died in Haiti and the Dominican Republic from flooding.
The storm's remnants were forecast to bring several inches of rain to Alabama, Mississippi, eastern Louisiana and Tennessee on Sunday and Monday.
President Bush declared four hard-hit Florida counties disaster areas. The declaration makes funds available for emergency work and repairs to governments in Brevard, Monroe, Okeechobee and St. Lucie counties. More could be added later.
On Sunday, Florida Gov. Charlie Crist visited the site of heavy flooding in Wakulla County in the Florida Panhandle.
"I think this storm is close to being over," Crist told Red Cross volunteers. "I don't know of one staying here longer."
Crist stopped at the Riverside Cafe on the banks of the St. Marks River, where a pole indicates the water level of past storms. While Hurricane Dennis brought 4 feet of water in 2005, owner Stan West said Fay brought only about 6 inches.
"God was good to us," West said as he served Crist fried and raw oysters.
But forecasters said West and others along the St. Marks River and similar waterways may not be in the clear.
The river was recorded at 6.9 feet on Friday. On Sunday, it was at 12.89 feet, and it may take some time for the water to recede, said Todd Hamill, a forecaster at the Southeast River Forecast Center in Georgia.
The 310-mile St. Johns River, which runs north from central Florida to the far northeast corner of the state, is the most swollen it has been since the 2004 hurricane season, Hamill said. On Wednesday, it was at 3.5 feet at one point. Four days of heavy rain later, it was at 10.2 feet.
"The water had nowhere to go," he said.
In Timber Lake, the 300-home subdivision near Tallahassee, firefighters, police and sheriff's deputies spent Saturday night and all day Sunday ferrying people out after a large holding pond overflowed.
As many as 100 homes were flooded, while the rest were cut off from the subdivision's only entrance road. Water rose near the tops of mailboxes, stranding several cars, and residents were told it could be days before power was restored because transformers were underwater.
Lagorris Smith, 35, went back to his house by boat to get his 6-year-old daughter's backpack and school work. He had gotten his family out just as water reached his house, though it had not flooded by Sunday evening.
"We were blessed," said Smith, who said he had never seen such bad flooding in seven years in the subdivision.
Jason Russell, 34, closed Friday on a new house in a different neighborhood. He hadn't intended to move until next weekend, but after the power went out, he spent Sunday emptying his Timber Lake house.
"We're getting the hell out of here," said Russell, whose face was covered in sweat as he and his brother-in-law hauled a small freezer up a dirt path and through the woods, the only way out of the subdivision besides the flooded main road. "This sucks."
In other states, the rain was welcome. Some areas expected to get heavy rain have been suffering long-term drought conditions.
In Huntsville, Ala., National Weather Service senior forecaster Andy Kula said the five-day rainfall projection through Friday - 6 to 7 inches south of the Tennessee River and 3 to 4 inches north of the river - would spread out and was not expected to create a flood problem.
"We need something like this to recharge the soil. It probably won't be a total drought-buster," Kula said.