Service on the No. 1 was suspended between 14th Street and South Ferry, and there were extensive disruptions to the 2, 3 and 5 lines. Train service had resumed normally as of 3:50 p.m., said NYC Transit spokesman James Anyansi.
The break shut down the renovated South Ferry terminal in lower Manhattan shortly after Gov. David Paterson and other elected officials attended a ribbon-cutting ceremony for its grand reopening.
The station - the terminus of the No. 1 line - was opened at noon and closed because of the water main break around 12:40 p.m.
The new station replaces one built in 1905. That station accommodated only five cars, so riders had to walk to the front of the train to get out. The new station's platform allows all 10 cars to open.
The city's Department of Environmental Protection was investigating the cause of the water main break, spokeswoman Mercedes Padilla said.
In addition to the subway problems, two lanes of traffic were closed on Varick Street.
NEW YORK AND TRI-STATE AREA NEWS
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