Early on, the effects of Hurricane Sandy seemed quantifiable, if unprecedented, for New York City’s transportation system: flooded tunnels, entire stations temporarily wiped from the subway map, and, according to initial estimates, about $5 billion to rebuild all that was damaged.

But in the year since the weather forecasts first turned ominous, sending workers scrambling for sandbags and plywood that would in too many cases prove no match for the storm, the Metropolitan Transportation Authority has been forced to adapt in ways few could have predicted, setting off a procession of management changes, unexpected system failures, and, at times, fiscal uncertainty.

The consequences, officials acknowledge, will be felt for years, most acutely in the form of persistent service disruptions that will dog riders across the system — in areas directly touched by the floods and in others where storm-related triage could delay scheduled work intended to keep the subways in a state of good repair. It can feel like far more than a year ago that the authority was cast as a hero of the storm, restoring much of its system more quickly than expected while other transit agencies flailed.

“The downside to it,” Thomas F. Prendergast, the authority’s chairman, said of the initial praise, “is I think sometimes it leaves people with the impression that we weren’t damaged that bad.”