UPDATED | Floodwaters rushed through Lower Manhattan on Monday night, inundating some tunnels and likely leaving New York City's mass-transit system hampered for days.

No clear estimate was available, and the Metropolitan Transportation Authority did not provide a timetable for reopening the subways. But the extent of flooding and the height of the storm surge appeared likely to meet or exceed the level of a 1992 nor'easter that forced the temporary closure of subway tunnels for both the MTA and the Port Authority of New York...