In eastern Pennsylvania, up to 200,000 people were ordered to evacuate their homes on Wednesday amid fears that the Susquehanna river could spill over flood defences.
A huge swathe of the northeastern US from Virginia to New York has been affected by the flooding and up to 40 centimetres of rain fell in some areas.
Helicopter crews in Pennsylvania have been sent to rescue residents stranded on rooftops by the flooding.
Ed Rendell, the governor of Pennsylvania, said: "We were afraid of a New Orleans-type situation where we just couldn't get people out."
Thousands of people were evacuated from communities across New York state, and whole villages north of Binghamton County were cut off by high water levels.
James Adams, who left his family's home near Binghamton after watching their shed float away and their cars become submerged by water, said: "We lost just about everything - the cars, the clothes, even the baby's crib.
"I'm not sure what we are going to do."
A state of emergency has been declared in 46 Pennsylvania counties and national guard troops patrolling in some areas have received orders to arrest anyone breaking a 9pm curfew.
George Pataki, the New York governor, said he would ask the federal government to declare a state of emergency for his state and said that he was bracing for the worst because waters had not yet crested.
"We have never seen a natural disaster this bad in the state of New York," Pataki told CNN.
The mayor of Washington DC also declared a state of emergency in the US capital.
Earlier this week, the authorites in Washington DC closed a number of government buildings, including the justice department and the national archives, after they were affected by the flooding.