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Matt Rourke, Associated Press
A person turns back from crossing floodwaters, Thursday, Sept. 8, 2011, in the Manayunk neighborhood of Philadelphia. Widespread flooding brought on by the remnants of Tropical Storm Lee was being blamed for two deaths in Pennsylvania, where inundated communities were evacuated and state offices closed down on Thursday because of the rising waters.

WILKES-BARRE, Pennsylvania — Nearly 100,000 people from New York to Maryland were ordered to flee the rising Susquehanna River on Thursday as the remnants of Tropical Storm Lee dumped more rain across the Northeast, closing major highways and soaking areas still recovering from Hurricane Irene.

At Binghamton, New York, the wide river broke a flood record and flowed over retaining walls downtown as more than 8 inches (20 centimeters) of rain fell in some areas. Road closures effectively sealed the city off to outside traffic as emergency responders scrambled to evacuate holdouts who didn't heed warnings to leave neighborhoods.

Most of the people ordered to evacuate their homes were about 80 miles (128 kilometers) downstream in Wilkes-Barre, where the river was projected to crest later Thursday at 41 feet (12.5 meters) — the same height as the levee system, officials said. Residents were ordered to leave by 4 p.m.

In Port Deposit, Maryland, rising water levels at the Conowingo Dam forced officials to open the floodgates and order the evacuation of most of the Susquehanna River town's 1,000 residents.

Evacuation orders were issued Wednesday to some 20,000 people in Binghamton and neighboring communities along the Susquehanna. More than 70,000 residents in Wilkes-Barre and Kingston were told to leave. So were people in about 170 homes about 90 miles (145 kilometers) downstream in Harrisburg, where crews put sandbags around the governor's mansion.

Wilkes-Barre Mayor Tom Leighton said residents should prepare for an evacuation of 72 hours and advised them to take clothing, food and prescription medicine. He also asked city businesses to close their doors by noon.

Water levels along much of the Susquehanna were expected to be at their highest since 1972, when Hurricane Agnes devastated the river basin.

At least nine deaths have been blamed on the storm that hit the Gulf Coast last week as Tropical Storm Lee and has slogged northward ever since. Four people died in central Pennsylvania, one was killed in Maryland and four others died earlier when Lee hit the South.

Roads and highways closed around the Northeast, including sections of New York's Interstate 88, which follows the Susquehanna's path. In Philadelphia, flooding and a rock slide closed the eastbound lanes of the Schuylkill Expressway, a major artery into the city, and it could take hours for the road to reopen.

New York's Thruway Authority expected to close a 105-mile (169-kilometer) stretch of its busiest east-west highway, Interstate 90, because the nearby Mohawk River had overflowed its banks in some areas.

Wet weather followed by Hurricane Irene and its remnants have saturated the soil across the Northeast, leaving water no place to go but into already swollen creeks and rivers. Some areas hit by the latest storm were still feeling Irene's effects: A shelter in Paterson, New Jersey, still had Irene evacuees.

In New Jersey, there was some flooding along rivers including the Passaic, which breached its banks during Irene and caused serious damage. Heavier flooding is expected Thursday.

A flood watch was in effect through Thursday afternoon in soggy Vermont but officials on Thursday said that rain has caused only minor problems in the state. Parts of the state are still recovering from flooding from the remnants of Irene, which was a tropical storm by the time it swept over the area.

Meanwhile, in the open Atlantic, Hurricane Katia brought rough surf to the East Coast but was not expected to make landfall in the U.S. Tropical Storm Maria also formed Wednesday far out in the Atlantic, but it was too soon to tell if and where it might make landfall.

Hill reported from Oneonta, New York. Contributing to this report were Associated Press writers Mark Scolforo in Hershey, Pennsylvania; Randy Pennell in Philadelphia; Chris Carola and Rik Stevens in Albany, New York; and Jim Fitzgerald in White Plains, New York.