Commuters into New York City endured long waits and crowded trains, giving the recovering commuter system a stress test a week after Superstorm Sandy ravaged the New Jersey and New York coast lines.
Trains were so crowded Monday on the Long Island Rail Road that dozens of people missed their trains.
With PATH trains between New Jersey and Manhattan still out, lines for the ferry in Jersey City quickly stretched to several hundred people by daybreak.
Key subway lines connecting Manhattan and Brooklyn under the East River had been restored after a week off-line.
But officials warned that other water-logged tunnels still weren't ready for Monday's rush hour and that fewer-than-normal trains were running.