Some 10,000 residents near Binghamton were ordered to evacuate early Thursday after the Susquehanna rose 18 feet in just 24 hours, officials said.
"This is a major flooding situation," Gov. Andrew Cuomo said at a news conference. "This is nothing to be trifled with."
Cuomo's warning came after he surveyed the flooding by helicopter to get a first-hand look at the damage. State Sen. Thomas Libous warned flooding would be worse than June 2006.
The Binghamton Press & Sun-Bulletin said more than 1,000 people sought shelter inside Binghamton University's Events Center and West Gym. The facilities can accommodate about 3,000 evacuees. Evacuees also headed to Red Cross shelters, the newspaper said.
The river was expected to rise to near 25.1 feet Thursday evening before starting to recede. Route 17, the Southern Tier Expressway, was covered by water and mudslides forced some closures on Interstate 88 and I-81.
The flooding was worsened by rain from the remnants of Tropical Storm Lee, which dumped torrential rains on the Northeast and Mid-Atlantic regions. The National Weather Service issued flash flood warnings from Virginia to New York.
An alert issued early Thursday morning said the Elk Lake Dam in Susquehanna County was at risk of "imminent failure" and urged people living below to move to higher ground immediately.