The Susquehanna River has reached record levels in Pennsylvania and New York state, swollen by torrential rainfall from Tropical Storm Lee.
US President Barack Obama has declared a state of emergency in both states, bringing federal aid to affected areas.
The river rose a record 13 metres in Wilkes-Barre, Pennsylvania, on Friday but later receded.
The BBC reports flash flood warnings are still in effect for south-central Pennsylvania and Maryland.
Tropical Storm Lee made landfall near New Orleans a week ago. It brought torrential rain to many areas as it swept north-east, killing at least seven people.
The Wilkes-Barre levee system withstood the cresting Susquhanna river, although much of the damage was concentrated in the surrounding areas.
More than 75,000 people were told to leave.
In Binghamton, New York, the river broke a record by spilling over retaining walls. Flooding closed a major highway near the city.
Some 20,000 people remain under evacuation orders in Binghamton.
Evacuation orders are expected to stay in place until Sunday or Monday.
Sandbags have been put around the governor's mansion in Harrisburg, the capital of Pennsylvania, 90 miles down river.