“There is a lot of rain to come,” said Jeff Byard, associate administrator for response and recovery at the Federal Emergency Management Agency. He spoke during a news conference on Saturday where a snapshot of the federal response so far emerged. The Coast Guard said 43 aircraft had rescued five people. The Army Corps of Engineers was engaging in a $6.1 million response, monitoring federal dams, helping with rescues, and deploying pumps and portable barriers.

And while officials pleaded with residents not to try to drive on flooded streets, and warned that the slow-moving storm still posed a serious threat, they also began preparing for what will most likely be a long and costly recovery.

Some who had evacuated returned home on Saturday evening to survey the damage. Tanya Caulder of Coward, S.C., found a giant tree in her front lawn after spending two nights at a shelter. Fortunately, the tree had fallen away from the house and just missed the pump house, which her family used to get water.

But Ms. Caulder, who had stayed at the shelter with 12 relatives, said she was still worried about flooding. During Hurricane Matthew, she said, the nearby Lynches River had sent water into her mobile home. All 13 members of the family would be staying at the house that night, she said, since only her place still had power.

“But if I see water come up in the backyard, I’m out of here,” Ms. Caulder said.

President Trump’s major disaster declaration, approved Friday, paves the way for millions of dollars in aid for storm victims. David Maurstad, chief executive of the National Flood Insurance Program, said the program was readying to address claims.

In Wilmington, the waters of the Cape Fear River were gray and roiling at daybreak. With up to 20 inches of rain forecast, roads were flooded in some low-lying areas and along stream and river banks. Emergency authorities warned that widespread flooding was still a threat from the storm’s trailing bands.